JC, Biggs and Boba are definitely great ships that can last you well into the late game. Mace as a capital ship is a bit less frequent. Home One is mostly seen in early/mid game and Executrix takes over in most shards as late game comes along. Now with the addition of Chimeara, we may see it taking over, as early on it seems pretty great. It requires rebel ships (including Phoenix) to unlock by the way.
All that said, if you're looking for synergies and are thinking of keeping Mace as your capital ship into the long run, you should focus mostly on light side ships (more specifically Republic ships). However, note that the zeta challenge requires a certain amount of dark side ships, as well as Executrix, so prepare accordingly.
Ahsoka has a good ship that can last you a while with her dispell that comes in quite handy against opposing Biggs and Scimitar ships, so she won't be a lost investment. TFP is also a good ship, especially if you're looking at pairing it with an Executrix capital ship down the line. It's turn meter manipulation on dodges is crucial there. It also can put on target lock on its basic, so pairs decently well with Biggs. It has no protection however, so if it misses a few dodges it can go down quickly, but at least it's quite fast. FOTP is a good ship under an Executrix lead. I don't see it much outside of that however.
X-Wing and Clone Sergeant are less prominent in fleet arena, especially in late game, but they can nevertheless be used. I used GS' ship for quite a while at the start because I liked its out-of-turn attacks and its assisted special. Wedge also packs a good punch and can pair well with Biggs, but both these ships have dropped off my lineup since I switch from Home One to Executrix recently.
Vader's ship is great if and when you get there and Rex has a pretty decent ship as well. Almost everyone will tell you that Fives' ship is a must as a second tank to Biggs (though I don't have it and still do well).
To me Scimitar is a must as a first reinforcement, and most top fleet squads run it that way.
All-in-all, for now, you can probably use pretty much any make up and do well in fleet arena if you focus some resources on it and don't get too unlucky with your fleet arena draw. I would say that most important is to keep in mind what you'll need to complete the zeta challenge. Before the recent improvements to the fleet arena rewards (and the addition of TB), that was arguably the only viable use for ships in most players' minds.
Hope that helps a bit!
Cheers,