Don't worry about your pick, just take whatever character/unit you want to play as. It'll be fine. Only thing that really puts anyone ahead is having the Free Capture skill because it makes capturing units slightly more convenient, but like the other anon said, it's not a big deal.
As you say, there's a lack of guides, so knowing how to capture stuff is probably good:
You can only capture units attached to a ship. You can press triangle on the ship and switch pages to see what units it has inside. In most cases, you will have to get close to the ship which will prompt it to launch its units during its turn. Then destroy the ship. The units will have white flags, meaning you can capture them; they also won't fight or move, so you can just leave them there until you're ready.
In most stages, a Gundam will also be attached to a ship. If you do all the break triggers and the impact trigger, you need to use your EMOTIONS to convince the Gundam pilots. Shooting down the ship that went hostile *will* let you capture the attached Gundam.
Actually capturing is done by moving your ship close to them; when there are white flag units, a "capture" command shows up in its command menu.
There are two break triggers and one impact trigger on each stage. Do as many as you feel comfortable with. They launch a bunch of new units, meaning more exp, more money, and more units to capture. If you do the second, more difficult, option on a trigger, you will also spawn "secret" units, which is a small squad of a leader and some escorts. Shooting down the leader will cause the escorts to automatically raise a white flag, allowing you to capture them.
You pick up your captured units from the War Room -> Captured menu, where you have to select "keep" to actually be able to use the unit. Selling leftover units is a good source of income.
As for what units and pilots to use: whichever you prefer, really. It's not difficult enough not to.