As others have stated, the INT increases shouldn't be an issue if that is the route you choose.
For the spell-like abilities, I would look to make use of the Spell Mastery feat. As a DM, I could certainly see a player using a Wish to bump up a "Mastered Spell" to a spell-like ability usable once per day. A generous DM may even allow all of the spells mastered with one application of this feat to be upgraded to spell-like abilities with the use of a single Wish.
I think you are definitely on the right track as to how a wizard could best make use of a Wish to increase his effectiveness at what he does. As a player, I am a huge fan of innate powers and abilities as opposed to magic items which can be taken away, lost, dispelled, etc.
Cheers,
-War Golem