For planet hopping, there was a really good discussion on that here:
http://arcengames.com/forums/index.php/topic,2953.0.html My suggestion is transports.
Regarding what percentage of planets to take, I wouldn't worry about a percentage. It's more a fixed number of planets; some players will tell you to stay within 6-8 total planets if you can, personally I trend more towards 20-30 in an 80-planet game. It's up to your playstyle.
If the AI is giving you a hard time on defense, then that probably means you haven't upgraded enough in turrets. Some of those, like laser turrets, are cheap in knowledge and really powerful. In general, a turret is stronger than a mobile ship -- just with the drawback of being immobile. Also be sure not to neglect tractor beams. And, if you can create a "clump" of your planets to protect yourself so that you have fewer openings into hostile space, that is always a plus (but not always possible). Lastly, if your harvesters are always dying on a planet or two, you might consider harvester exo-shields. They'll hit your economy, but can be worth it for the safety -- depends on your style, I just rebuild them. Oh, and I guess really lastly, I love spider turrets because they do engine damage to incoming ships, which is invalable for stopping especially small raids in their tracks, but even slowing down larger raids.
For your question about neutralizing a system as a threat without increasing the AI progress too much, I'd suggest just capping the special forces guard post (if any), the train station (if any), and then all of the smaller guard posts. The AIP will go up slightly from the specops post and train station, but it's very small compared to the benefit you get. Search for "neutering planets" planets for more info on that sort of thing, but I'm sure other players will drop by with their thoughts, too.
For the mobile repair station, there's no way to stack ships, and really what you're seeing is something of an exploit (not that it hurts anything, but it's annoying to you, as you've noted). Better solution: use the space tugs off the mobile repairs stations, so that your guys get yanked out of battle when they are too hurt, brought back and repaired, and then sent back into the fray. In terms of knowledge that is free (since you already have the mobile repair station), and it will save you a ton of time (and lost units) during, as well as after, battles.
Hope that helps!