Most of the core prestige classes are on the weak side, so it certainly wouldn't be unreasonable to make them a little stronger.
The only thing I'd be mindful of with the Assassin is that due to the change in the way the skill system works between 3.5 and PF, it no longer has any meaningful prerequisites. Anyone with an evil alignment can qualify by the 5th level with minimal effort, so ensure that you're comfortable with a fifth level fighter in platemail or a 5th level ranger who is a crackshot with the longbow becoming assassins while keeping full BAB.
Well I know that it would certainly be nasty to have it turned against a potential PC but I still think it would be an appropriate change. Plus I really want to play a Strix assassin. Swoop/kill/flyaway. I think 5 levels of ninja for fast steath and the invisibility thing would be excellent along with the scout archetype.
I had a player who wanted to play a True Neutral Assassin that didn't suck at actually killing stuff.
Thanks for giving me a houserule idea, I'll just raise the Prestige Class' BAB to full so it could actually do things.
Also, I find it kind of funny how the Red Mantis Assassin totally stole all the normal Assassin's thunder now in Pathfinder.
Assassins could cast spells in 3.5e, so they gave that ability to the Red Mantis instead. The Assassin got the scraps of the class.
Cheapy, I know that sneak attack is supposed to supplement med BAB, but it seems that sneak attack has alot of restrictions on it and I think that a straight fighter would still way out damage the SA. My main thing is that I feel the Assassin PrC is too weak for a martial class and I like the idea of them excelling at killing. I would think that someone who focuses intently on superduper killing should be good at hitting.
Anyway, would trading down from 5d6 to 3d6 be enough for you to sign off on full BAB.
also I dont like spells much. I am happy the PrC doesnt have them any more.
I guess it would have SOME purpose other than "we really didn't think about rogue talents during core and realize we could just make these special abilities ones" (and from the sheer number of utterly useless ones and a couple being worse than nothing, not outside of core either, but for another topic).
I'd prefer it got its spells back instead though. I'm a big fan of the idea no character, even the martial type characters (except possibly at really low levels) is truly "mundane"