Not that scary at all - that is how all programs are. Think of it like this - the exe is the start button you push to then have it compile all the instructions given (es/esp/ess + all replacers) to then result in the game you play. If out of place then yeah issues will arise. Like a missing master - the game calls for references that don't exist = crash. It seems overwhelming because people find it so easy to add new mods, just not test them.
And so there are several factors that can lead to ctds: Hardware issues (including drivers and hardware malfunction), game settings (including bad ini edits), bad replacers (corrupt custom meshes can crash your game), and of course bad edits in plugins themselves.
As for bad edits nothing beats http://cs.elderscrolls.com/constwiki/index.php/TES4Edit_Cleaning_Guide. This is more understood with Oblivion and not so understood here. (since people will jump on me for not saying ... don't clean MMM or other overhauls or the UFP).
The whole master update thing is another, I think, red herring of an issue. The problem is that major mod makers don't want to wait for this company to finish their patching of the game and so forge ahead with mods that then get invalidated with the next patch. it so happens patch 5 was a debacle and the temporary work around was to create MasterUpdate instead of just waiting for the next official update. This company will only update so much, so it is not like a long wait. Anyway then a whole school of thought arose that it was necessary. I've never used it and the few times that I did use it - it didn't solve diddly.
People also advocate for using http://www.gamesas.com/index.php?/topic/1117083-merged-patch-or-bashed-patch-or-both - and granted the bashed patch was not available for a while, but now it is and it is a more sophisticated problem solver than the merged any day.
The motto is
my load order is my responsibility. Take http://www.gamesas.com/index.php?/topic/1165533-need-serious-load-order-help-cant-find-whats-causing-this/ for instance. He is trying to combine all major overhauls that even basic reading of readmes would reveal they are not compatible.
It is best to go slow when learning how to mod these games from bethesda - and while it may be possible to add much and there is much to add - the more you add the more potential issues could arise.
Sometimes they are timebombs that may not cause issues until you visit a specific area in the game. It is just like that.
[edit] also let me add that by cleaning mods, using a bashed patch (wrye flash), and testing each mod before adding a new one I have a very stable load order which very much does include the UFP:
Spoiler Active Mod Files:00 Fallout3.esm01 Anchorage.esm02 ThePitt.esm03 BrokenSteel.esm04 PointLookout.esm05 Zeta.esm06 Unofficial Fallout 3 Patch.esm [Version 1.2.0]07 StreetLights.esm08 Inventory Access.esm09 IMCN.esm0A Destruction.esm0B PointLookout-FollowersGetToGo.esm [Version 2.]0C Impervious Power Armour.esm0D CRAFT.esm0E CALIBR.esm [Version 1.4]0F xCALIBR.esm10 xCALIBRuniverse.esm11 Project Beauty.esm12 Refurbishes [ALL].ESM13 CubeExperimental (EN).esm14 Project Genesis.esm [Version 1.00]15 FO3 Wanderers Edition - Main File.esm16 Mart's Mutant Mod.esm17 Companion Core.esm18 Companion Share & Recruit.esm19 RobCo Certified v2.esm1A Wasteland Whisperer v2.esm1B Enhanced Weather - Rain and Snow.esm1C Xepha's Dynamic Weather.esm1D DCInteriors_ComboEdition.esm1E Zumbs' Overhauled Real Time Security.esm1F SS Master File.esm20 Ambient Temperature.esm21 Unofficial Fallout 3 Patch - Operation Anchorage.esp [Version 1.2.0]22 Unofficial Fallout 3 Patch - The Pitt.esp [Version 1.2.0]23 Unofficial Fallout 3 Patch - Broken Steel.esp [Version 1.2.0]24 Unofficial Fallout 3 Patch - Point Lookout.esp [Version 1.2.0]25 Unofficial Fallout 3 Patch - Mothership Zeta.esp [Version 1.2.0]26 FireLightFix.esp27 DarNifiedUIF3.esp28 Ambient Temperature HUD.esp** Project Beauty- Broken Steel.esp** Project Beauty- Point Lookout.esp29 StreetLights - Wasteland.esp2A DoF-PureLow.esp2B TinCanCRAFTing.esp [Version 2.0]2C CRAFT - EnergyAmmo.esp2D CALIBRxMerchant.esp2E LMDExpandedHotkeysFO3.esp [Version 0.6]2F Princess Better Prompts v1pt1.esp++ Zombie Sounds V2.esp++ GeneratorSound.esp30 Moshman's Wasteland Ambiance.esp31 GalaxyNewsRadio100[M].esp32 RadioBlues.esp33 WAR_radio.esp34 People_Radio.esp35 InvasionRadio.esp36 KBATRadio.esp37 VTAP25.esp38 GhostRadio.esp39 mutantradio.esp3A LookoutRadio.esp3B RadioTenpenny.esp3C Radio Stutter fix.esp3D RadioHotkey.esp3E RadioHotkey_RadioBluesAddon.esp3F TCOS.esp40 CONELRAD 640-1240.esp41 Existence2.0.esp42 UPP - Pack 1.esp43 UPP - Pack 2.esp44 UPP - Original Perks.esp45 UPP - Experience Perks.esp46 UPP - Quest Perks.esp47 PreWar Book Titles and Perks.esp48 Combat Style Perks.esp49 NotSoFast.esp4A HeirApparent.esp4B NightmareRealm.esp4C MarkB50K_Wasteland_Patrols.esp4D tubRRCompound.esp4E Stealth Kills Enabled.esp++ Stealth Kills Enabled - Pitt Compatibility.esp4F Echo_BatteryCharger.esp50 HouseholdWaterPurifier.esp51 BlackWolf Backpack.esp52 GunnySack.esp [Version 1.3]53 1Animated Nightvision goggles.esp54 FNVFOV.esp55 Xepha's Radial Blurred Zoom.esp56 Directional PipLight HDR.esp57 Down Under.esp [Version 1.0]58 Expanded Megaton House V3.esp59 MaintenanceShed.esp [Version 1.3]5A merc.esp5B MoreMapMarkers.esp5C MaxLevelWorkaround-HP-BS.esp5D WastelandMastery.esp5E SkillCheck.esp5F Treasure Maps_Underground.esp60 Treasure Maps_Secrets of the Wasteland.esp61 Treasure Maps_Bobblehead Edition.esp62 Treasure Maps_A Fist Full of Caps.esp++ Destruction - Main.esp63 Destruction - Main - Statics.esp++ Destruction - DLC.esp64 Destruction - DLC - Statics.esp65 BusworldV1.05d.esp66 SS Enhanced Combat Maneuvers.esp67 MTC Wasteland Travellers.esp68 DCInteriors_DLC_Collectables.esp69 Rivet City Realignment.esp6A megalight.esp++ WastelandRecovery5.esp6B MovinOnUp3.0.esp6C Canterbury Estates 0.8 beta.esp6D FO3 Wanderers Edition - Main File.esp6E FO3 Wanderers Edition - DLC Anchorage.esp6F FO3 Wanderers Edition - DLC The Pitt.esp70 FO3 Wanderers Edition - DLC Broken Steel.esp71 FO3 Wanderers Edition - DLC Point Lookout.esp72 FO3 Wanderers Edition - DLC Mothership Zeta.esp73 FO3 Wanderers Edition - Alternate Travel.esp++ FO3 Wanderers Edition - Optional Restore Tracers.esp74 FO3 Wanderers Edition - Optional VATS Realtime.esp++ FO3 Wanderers Edition - Project Beauty.esp++ FO3 Wanderers Edition - Project Beauty (Followers Enhanced).esp75 FO3 Quest Patch - FWE + BS.esp76 WeaponModKits.esp77 WeaponModKits - FWE Master Release.esp78 WeaponModKits - OperationAnchorage.esp79 WeaponModKits - ThePitt.esp7A WeaponModKits - BrokenSteel.esp7B WeaponModKits - PointLookout.esp7C WeaponModKits - Zeta.esp++ Echo_UseBothGloves.esp7D AlexScorpion's and Weijiesen's Smoking Fun.esp7E SolarScorcher.esp7F Tactical Weapons by gRs Frederyck.esp80 ZL-ACR.esp81 ZL-SVD-CALIBR.esp++ InverseCombatKnife.esp82 Playing With Firepower.esp83 Dogmeat Leather Armor - CRAFT.esp84 Dragonskin Tactical Outfit.esp85 DragonskinBonusPack.esp86 Stealthboy Recon Armor - CRAFT.esp87 Powered Power Armor.esp88 PPA - Operation Anchorage.esp89 PPA - Broken Steel.esp8A PPA - The Pitt.esp8B PPA - Mothership Zeta.esp8C PPA - FWE.esp8D CALIBR Ammo Schematics - CRAFT.esp8E CRAFT Improvised Weaponry.esp8F CRAFT Improvised Weaponry - Unmodeled.esp90 DogmeatEssentialModv1.2.esp91 Move-Dogmeat.esp++ DogmeatStealth.esp++ ZORTS - Custom HP - FWE.esp92 ZORTS - Disable FWE activate.esp93 Companion Core DLC Addon.esp94 Wasteland Whisperer v2 Broken Steel Addon.esp95 RobCo Certified v2 Mechanist's Edition.esp96 RobCo Certified v2 Zeta Addon.esp97 Mr Smith's Scrapyard.esp++ tubURP.esp++ ThePitt-NoFireFollowers.esp98 ImmersiveHealth.esp99 FalloutFood.esp++ FalloutFoods - FWE Master Release.esp** Gunfire Sound Range Increased.esp9A EVE.esp9B EVE Operation Anchorage.esp9C EVE - FWE Master Release.esp++ EVE - FWE Master Release (Follower Enhanced).esp++ EVE Anchorage - FWE DLC Anchorage.esp++ EVE - FWE with WeaponModKits.esp9D Mart's Mutant Mod.esp9E Mart's Mutant Mod - DLC Anchorage.esp9F Mart's Mutant Mod - DLC The Pitt.espA0 Mart's Mutant Mod - DLC Broken Steel.esp++ Mart's Mutant Mod - DLC Point Lookout.espA1 Mart's Mutant Mod - DLC Zeta.espA2 Mart's Mutant Mod - FWE Master Release.espA3 Mart's Mutant Mod - FWE Master Release + DLCs.espA4 Mart's Mutant Mod - FWE Master Release + Project Beauty.espA5 Mysteriouswoman_corsetntrousers.espA6 Imp's More Complex Needs.espA7 IMCN - 5 DLC Merged.espA8 IMCN - FWE Compatibility and Ingestibles.espA9 IMCN - MMM Meats, Bloods, and Eyeballs.espAA IMCN - Ambient Temperature.esp++ PPA - IMCN.esp++ T3T_MiscItemIcons.esp++ ACRForFWE.esp++ SVDForFWE.esp++ DTOForFWE.espAB Zumbs' Smaller Condition Effect On Item Value.espAC Gifts4Kids.espAD NTFS.espAE Phalanx-Obedient-Dogmeat.esp++ lessviewdistance.esp++ PiPBoy Light Range x4.esp++ PiPBoy Yellow Light.espAF Enhanced Weather - Rainbows.espB0 Enhanced Weather - Weather Sounds in Interiors.espB1 Realistic Interior Lighting.espB2 Realistic Interior Lighting - BS.espB3 Realistic Interior Lighting - OA.espB4 Xepha's Dynamic Weather - Main.espB5 Xepha's Dynamic Weather - Anchorage.espB6 Xepha's Dynamic Weather - The Pitt.espB7 Xepha's Dynamic Weather - Broken Steel.espB8 Xepha's Dynamic Weather - Point Lookout.espB9 Xepha's Dynamic Weather - Rain.espBA Xepha's Dynamic Weather - Sandstorm.espBB Xepha's Dynamic Weather - Sandstorms Damage Armor.espBC Xepha's Dynamic Weather - Dynamic Sneak Bonus.espBD Xepha's Dynamic Weather - Green Tint Remover.espBE RobCo Certified v2 Omnipatch.esp++ RobCo Certified v2 Impervious FWE.espBF xCALIBRuniverse.espC0 xCALIBR - Alternative Path.espC1 xCALIBRUniverse - WMK.espC2 xCALIBRuniverse_FWE_FPS.esp++ xCALIBRammo_FWE.esp++ frederyck+FWE+xCALIBR.espC3 tubunarFWE.espC4 tubunarCombatFWE.espC5 Bashed Patch, 0.esp
I have about 5 more mods I want to add, but it will take me a week or more to get them in because of the testing phase on them to make sure that when I add them all I don't get confused and think I have to tear it all apart again. The thing is you will spend the time learning it all - just the choice is yours - do you want to learn it after failing over and over and getting confused and overwhelmed or do you want to take it steady and pace yourself?