First, forget about what other people say about territory battles, that is end game content, you are just now getting ready for the top tier content (tier 7 raids and heroes journey events), as far as i know. You will get to territory battles eventually, in a fairly short amount of time i might add, if you simply stay on target about your farming priorities.
Just so you know, i do not use first order, i do not even have kylo ren developed, so my knowledge of them is based on my fights with them in arena and galactic war.
Some may say that empire are better in arena than first order and they talk about counters to JT rey, but that is still just theory crafting right now, besides do you want to go for what is optimal or what you can have fun with? You decide that, i will simply say what is a more effecient use of your time and resources to get to that goal. So which faction do you think would be more fun for you? Though true, that empire AI is more effecient in arena, and that they have more debuffs and damage out of those debuffs than first order, first order is more crit based than empire is, but then FO has plenty of assist attacks or double/counter attacks. And just like thrawn can stop a toon for a while, KRU can also stop a toon for a while.
And to answer your second question, KRU in shipments/packs or shoretrooper... Well my opinion is that i would rather farm shoretrooper through his hard node, because i get both him and his ship, it is a very good ship, much better than empire tie pilot´s and gar saxon´s ships. So if i would be willing to spend crystalls or money, then i would spend them on KRU in stead of shoretrooper, because i think i would get more out of both toons that way.
As for the team being squishy and those things, well except for a few more toons than FO, empire is also fairly squishy, it is just that the damage from debuffs weigh that out in their favor, just like assist and double/counter attacks weigh it out in FO´s favor. So i would suggest pick one and go all in on speed mods.