You are not crazy in your assumptions. This is because older kits have bigger/thicker gates attached to the parts while newer kits have better production where they are thinner .

Where do you live ? i suggest you go to a nearby hobby store where a sifu can guide you. Some of these stores also have airbrush painting facilities, so you can try and also meet fellow modellers.

1. The discoloration is due to stress mark underneath the plastic surface, can appear if during the process of removing the nub marks your cutting tools is not sharp enough or cut too close to the parts. If done properly there shouldnt be any marks (or minimal), but now that its there painting is the quickest way of removing it.

2. Marker and hand painting is ok for small parts, larger parts require alot of skill and steady hands to look great. If airbrush is troublesome maybe can try spray can, can get those from ace or any hardware shop though do be careful of which brand and type you choose, some are industrial grade which will corrodes soft plastic like gunpla. Its not cost effective in the long run but for only 1 or 2 kits its a viable alternative.

3. Newer kits seams lines blend in with the panel line so those you dont need to cement and sand. Those that do however will ultimately requires you to do some painting to finish it off.

4. Gunpla metallic is all electro-platted, its different from normal color that is molded into the plastic itself. The moment you cut from the runner the inner plastic mold, usually black in color, will be expose and nothing you can do about that. Marker will never match back the color, you can try hide it with marker if the part is small it'll not be noticeable but if its a large area the difference in color will be obvious. Painting over it entirely with a metallic color of your choice is the best method.

Nope.

Did you check with this store ??

Invest for airbrush. The RM9-11 Mr.Hobby or Gaianotes 10ml bottle can last longer than spray canned.

I never go to spray top coat again.