It is very opinion base, but your mainstream companies use cheaper materials and hard dome tweeters which are raspy and very harsh. Companies to look at are RD, Focal, Rainbow, or older MB stuff.
Incorrect. The amp draws power from the battery. The alternator is what charges the battery. The battery is a power reserve and once drained you will drop voltage so low that the amp will shut off. Most amps will shut off at 10 volts. Capacitors are a waste of money and the biggest gimick to hit the audio market. The amplifier itself has (or should have) as many caps as needed to regualte voltage across the board. Your best fix is to get a gel cell like an Optima yellow top that has a slower discharge. Again, our Fusions only have about a 110-120 amp alternator. 1000 watts rms pulls 100 amps.
I highly doubt it is a true 2000 watt amp. You will only be able to run at most 1500 rms off stock and that is pushing it. I suggest no more than 1000 without at least a battery upgrade. What brand amps are those?
Alpine is one of the few companies still making decent headunits. You are only getting a true 15-20 watts rms out of the unit amp itself though. The ols RF subs are pretty good but the new ones are horrible. I would also get away fomr MB Quart now days too. Boston isn't too bad. Highs are a little harsh but mid bass is good.
If you don't care about door speakers or a true "audiophile" then a LOC will be fine. If you want to change everything out, there is a more expensive way of going.
You need a LOC (line out converter). Metra should have a harness to use sync with aftermarket decks now though. I would have to call and check but I am pretty sure my installer said they do.