I would have train stops at 2nd Ave. and Avenue B instead of at 1st and 3rd Aves. 3rd Avenue is a given as it's only a block away from Union Sq., and walking to Alphabet City is a bitch depending on how far in you have to go (good luck if you're going to Ave. D...). Also, when (if) the SAS reaches down there in Phase 3 anyway it would make the 14th St. transfer to the that much easier. Similarly, I would add 2nd Ave. stations to the , , and lines. No one's going to want to walk 2 avenues down to the Lexington Ave. stations when the SAS opens, and 2nd Ave. is populated enough to warrant stations too. I doubt those are possible under existing conditions though.
As has been mentioned earlier in this thread I would have stations at 5th Ave. - 63rd St. , Union Ave. (closing Hewes and Lorimer) and 103rd St. .
Is a station at Allerton Ave. necessary? It's really close to Gun Hill Rd. as it is. I also don't think it's necessary to add any more 28th St. stations since you're never more than 5 blocks away from a station between 23rd and 34th streets. You don't want too many stops as that just makes commuting slower.