If you are going to spend any time onboard, you want a good head with a door, unless you don't want to ever take women along. Some heads are so small they are really just storage compartments. If you are going to do any horizontal dancing, a head under the V-berth is a real bad idea. I suggest a vacuflush head as an absolute requirement.
Staggered engines. Side-by-side is a bad idea if you intend to buy used.
Also, if you are buying used, carbs are way better than EFI. The opposite is true if you buy new and turn the boat within a few years. EFI leads to impossible to trace weird bugs. Carbs are very easy to diagnose, cheap to fix and maintain, and work GREAT on boats.
Stepped hulls are quite a bit more fuel efficient (about 20%) and faster. But poorly designed stepped hulls work poorly: they may lack directional stability, they may porpoise. Fountains work well because they constantly improve the hulls. Most builders change their molds very, very rarely, and the chance of getting steps right the first time is quite low: hence the multitude of horror stories of ill mannered step hulled boats.
Make sure the structure will hold up. Few boats are built as well as Cigs or Fountains. Take the boat apart as much as you can, and look at deck joints, bulkheads, stringers, how things are mounted, everything.
Finally, always consider a longer boat. Its really no harder to tow a long boat than a short one. A 42 may be no more complicated, and therefore no more expensive to own, than a twin 28. A longer boat is much smoother, carries load better, provides more room to work on the engines and systems, and more room to play.