I am really only interested in the Imperial ships, is this similar to X-wing in that some upgrades are only available in one factions ships, and are usable on the others?

Correct. If you focus on only on faction, you will miss out on some of the best upgrades

Correct. If you focus on only on faction, you will miss out on some of the best upgrades

Maybe best wasn't the right word, but there are some that he wouldn't have.

Leading shots is coming in the interdictor so that won't matter anymore lol

Apt and xi7 are the main ones missing from imperial expansions but they have suitable replacments in Heavy turbolasers and ACM so really you don't need Rebel expansions at all unless your looking for extra copies

You can get Leading Shots alt art cards on eBay for pretty cheap right now (3 for less than $3 shipped), and you'll likely be able to pick up XI-7 alts soon, too. APTs are the tough ones, because Raiders LOVE APTs. Nothing like throwing a double-arc that does a guaranteed two face up damage cards to anything.