No point limits - the players earned their merit points, let them spend them!
Increased point costs for increased point limits - having more then three weapon skills capped will cost progressively more to do then the first choices.
Individual choices per job - each job has to unlock the weapon skills individually, but each job can unlock up to three.

Any of these would be awesome. The more I think about it, the less I like this whole system they have for these WS.

The only reason I could think of to put less than 5 merits in a chosen WS, is if it was only needed to proc.

If that is the case, then this is the worst system ever.

If not, then This still sucks real bad.