Strength requirements for big guns, perception for small guns, perhaps intelligence for energy? I'd go for something like that. The merge wouldn't even bother me if something like that occured. So long as overall we don't winde up with an even less balanced skill system and level cap.
I know they've said the game will go up to thirty, but that won't really be a problem if we get fewer points and more skills to dump them into.
Strength for all weapons would suffice with heavy weapons being wielded by only particularly strong characters you'd eliminate the problem of sneak characters the occasionally pull out a mingun and clear off a room full of heavily armed Nightkin.
Energy weapons is still separated from Firearms, and I personally don't think that small arms need a requirement at all.
I really doubt that the Obsidian team can pull off a system even less balanced than Fallout 3 anyway.
To be clear, I'm not thinking of the requirements as hard thresholds for use, I'm thinking of them as tiered consequences, introducing things like increasingly severe gun sway or increased critical failure rate.
[edit]: After thinking about it for a minute, I like your idea more than mine.