I chose magick for my battlemage, since most of his major skills are magick. I had thought about choosing combat since it would give my heavy armor, block, and blade skills (in which all three are major skills) a nice boost, but I thought nah, since I have mostly magicka skills, and it would be the wiser choice to choose magick as my specialization.

I really think... if you are, infact talking about specializations (aka, Combat, Stealth, and Magic)... the only difference is the RATE at which those level. I think they level up faster or something.

Once again, not a big deal in vanilla (Not that I have experienced)

However, I see in other posts that you have specific mods. I cannot help you much in those cases and someone else more familiar with the mods may be able to help

Yeah, I'm running FCOM.

FCOM doesn't touch character leveling in any way. For a hybrid character like Battlemage my recommendation would be to use http://www.tesnexus.com/downloads/file.php?id=13879 to control character leveling. In my experience Realistic Leveling is well suited for hybrid, multi-class characters. Specialization, Favored Attributes and Major and Minor Skills are much less important in Realistic Leveling, allowing the player to do pretty much anything they want with the character at any time without worrying about class restrictions.

I would also recommend http://www.tesnexus.com/downloads/file.php?id=14304 Progress allows you to control the speed at which skills level up to within a tenth of a decimal point. For magic users it has the additional advantage of granting a small bit of magic skill advancement for missed spells.

I don't wanna add any mods in fear that I might screw up FCOM. Last time I installed Darnified UI after FCOM, I somehow messed up the game.

I don't see how that's possible. The two mods don't overlap or conflict in any way. What exactly was messed up after you installed DarN?

I don't have any mods,but I choose specialization by wich combat skill I will use the most.
If it's destruction,illusion or any other magic skill I use the magick specialization.
For blade,blunt or h2h I use combat,and well you get the picture.

Game kept crashing after 2 or 1 minute into the game, and it always gave me this error when I launched OBSE. I actually had two other things installed that were minor, like the elven map, and I think the color enemy bars. Even after uninstalling those three, I still continued to receive the same problem.

Again, the problems you're talking about don't have anything to do with the mods you mention. Neither FCOM nor DarN uses OBSE.

I can understand being wary of mods, but don't blame FCOM or DarN for the problems you're having. Why are you running OBSE? Are you using a mod that requires it? If not, you shouldn't be using it.