Do you have any proof that your points are true with the Fallout 3 engine, or you're making assumptions based on your experience with Oblivion?
Let's go 1 by 1.
1) Breaks backwards compatibility with saves.
The mod changes names. Ergo, game-wise, it's a different mod, Items of the mod are eliminated from inventories, new npcs reset, quest and script variables are reset. If the mod added perks, the game will refuse to load. You could name them as esps, but then you make point 3 even worse.
2) Doubles the amount of mods in the load order.
If you transform every mod into an esm+esp pair.
3) Increases the chances of PEBKAC errors with load order, meaning modders will be annoyed by idiots more than before. This is highly undesireable.
The userbase is full of idiots. Anyone that reads mod comments and troubleshooting threads can confirm this. They even PM you to ask you about something that's stated on the first line of the description.
Currently, esms are reserved for DLCs and true master files, files that have a very good reason to be there.
Now you add a bunch of mods that are esm, thus, can load before these master files, meaning idiots will have more chances to get mods loading before masters, heck, even before fallout.esm itself.
Add moronic and non-working tools like FOMS to the mix. I seriously do not want to troubleshoot that.
4) It won't be automated and work right. It is something that ought to be done and adjusted by hand.
Automated jobs must adapt to most situations (and are a PITA to do that way), yes it'll get the job done, but there's little chance it will do an optimized job. Exceptions, specially at lower level tasks exist, but on the esp->esm+esp pair conversion, it wont be so pretty.
( 1.0.0.15 + Fakepatch + Lil Boy
or
1.4 )
+
BS's FAKEPATCH + Clear Waters.
Both methods have been confirmed to work. Yes you loose a pretty npc ai change and the ability to use the new toy in geck, but you have something compatible with any mod made pre-cluster[censored], and any mod adapted to the cluster[censored] will still work. On the user side of things, i'd rather explain 100 morons how to use fakepatch, than explain 100 morons how to convert his mods to esm, and tell them why are the mods failing. The repercussion of this is wide. Average idiot user downloads mod, gets crash, downrates mods and trolls, asks help on 8 forums at a time. VS, user asks how to use fakepatch. You can even make one step by step guide and re-post it in every thread. The damage made by the panicking pack is lessened through the fakepatch route
Now to other posters.
Still if 1.5 does somehow manage to make esms communicate better and whatnot, if new objects in esms work correctly and older problems can be fixed with the upcoming version of FO3EDIT, and vanilla DLCs prove they can add everything via esms just as well, and also given the fact that only specific types of mods and not all would require esmification, then would it be fair to say perhaps esmfication is the most viable (If also painful) method should 1.6 never come?
Yes and no, read reasons above.
In fact this (or very similar) bug affects esm's too. Just in another way. Fallout3.esm's references deleted by another esm appear on second visit. Bethesda's very own Broken Steel is affected by this. They deleted some Enclave soldiers on some Enclave camps to replace with newer variants. Those deleted soldiers now appears even before progressing in main quest.
Did the morons at beth learned anything with the pitt's horrible circle of death issue?.
Never. Delete. Anything. From. Master. File, Use. Disabled. At. Start. Or. XMarker. Dohickey. They should be made to repeat that phrase a few hundred times after waking up.