With the changes and upcomming Refits comming out, I think that Tier 3 is lopsided. Nebula and Excelsior are not really +1 ships, but there being shoe horned in to fit that place. I just hope that this is a temporay measure and a true +1 Heavy Cruiser and Research Science Vessel get added. As well as an Advanced Heavy Escort and it's Retrofit, and Retrofits for all of Orginal Tier 3 ships. An additional Tier 5 escort would also be nice as well.
Nebula and Excelsior are both physically different from the orginal Tier 3. +1 has in the 3 released ships and 4 planned ships been a new skin on the orginal, special console power, extra console slot and higher ranked BO. Nebula and Excelsior also have modified stats especially in the Nebula's case. Both are almost already +1. Also both were made into Tier 5 Retrofits which makes the Retrofit captain skill more valuable since they function differently from the other Tier 5 Retrofits.
In a fair world, an Advanced Heavy Escort, Advanced Heavy Escort Retrofit, Heavy Crusier Refit, and Research Science Vessel Refit would all be added. In a perfect world, Heavy Cruiser, Heavy Escort, and Research Science Vessels would have Tier 5 Retrofits as well.
Doesn't really pertain to the bonuses etc. but I would really love to see the soft canon TOS Dreadnought as a tier 3.5 ship. Its was only ever shown in the TOS tech manual and a handful of novels, but the triple-nacelle look on the connie frame always struck a chord with me. Some of the drawings I've seen with TMP nacelles and hull stylings we just out-of-this-world gorgeous, minus the doofy triple and rear-mounted deflector dish (but, on the other hand, fore and aft firing arcs for deflector abilities?....interesting concept).