Can I remove plugins that I don't like from the mod list? (e.g. I don't want to play with Super Soldiers or Jedis)

Yes, you should be able to safely remove any plugins / RPGO class mods that you don't like. However, check closely that you do not accidentally remove any dependencies for other mods. AML should help you to figure it out.

How do I get access to Jedi equipment?

This mod makes all the lightsaber gear craftable, you unlock the first tier after researching the stun lancer autopsy (second tier = Mag Weapons, third tier = archon autopsy)

How do I get access to the super soldier armors?

This mod makes all the super soldier armors single craftables. The tier 1 armors are craftable from the beginning of your campaign. To unlock Tier 2 and Tier 3 you have to research the 2 special armor kinds (e.g. to unlock Tier 2 of the Super Soldier armors you have to research the Spider Suit and the E.X.O. Suit)

I do not want to rely on RNG to get jedis and hero classes!

Play with Commanders Choice and Origins Second Wave Options enabled and disable random pool. You can then select everything you need to get access to the hero classes.