It really depends on what you want to do, but if you want a sweet combat ship, start with the Swamp Rat for its overcharge ability, add the Krembler for regeneration, and put it all into the Slow Leak, which can hold two d20 missiles...
Now I like to mine, so my dream ship is Easy Tiger for Tac-x re-rolls, Gaiden for the evasive thrusters, and finish with the Long Haul's shuttle to make deliveries.
If you are running long routes, try Puddle Jumper for longer space-keeping capabilities, Lone Drifter for extra movement, and for the finale, Cold Phoenix for Wormhole action.
All these are specialist ships, though, so it matters a great deal what other players are building... your plans should be flexible.
I like Easy Tiger for the reroll ability because it also works with missions. I also like the Numerator because getting extra movement when you need it is always good. Swamp Rat is great for the initial hold space, too.
I like all 4 of the new ships in the expansion - the level 1 ship has a really fun power that's quite good, the level 2 ship has a great movement power, and I also really like the level 3 ship for energy gain, healing, and hold space for a tier 3 shield. The other level 2 ship that comes with the Sellsword Mk II is great for efficient combat too.
Cold Phoenix is both my favorite ship model and my favorite ability. We've always played Replication Drive with what is official errata in the expansion, and it is a pretty close second. Both ships have abilities that are versatile, and that's important in a sandbox game.
Oversurge is my favorite at T1 by the largest margin at any tier. Tac-X and Energy Scoop tie for second... however Disruptor Field has gained a serious amount of credit in my estimation, I just haven't used Ghoststalker that many times since I changed my mind about it, so I honestly expect it to overtake second at some point.
Auto pilot, and Regeneration are my favorite at T2. However Tier2 ships/abilities are the least important in the long run. First tier ships are obviously important at the beginning of the game, and T3 abilities have the most impact. Unless you routinely play 10-15fp games (and I do not) the second tier is usually just a quick bridge to getting to T3, and ultimately has the least impact on the game.