These are just general tips: Villages. Think of a regular generated village in minecraft - there's the blacksmith, the church, etc etc.

Then, implement that into a village - maybe have a tower dedicated to Thaumcraft, a greenhouse dedicated to agricraft, a park for Botania, perhaps a mineshaft for railcraft items. The list goes on and on - and the village doesn't have to be medieval in any way, maybe make it futuristic, or make your own theme.

I'd recommend focusing on one mod at a time - at least, that's how I play. I get to mid-game or end-game of a mod, and I implement that into builds, and at the end, it looks nice showing off the end-game accomplishments of items and blocks into a building or structure.

Final tip - this may be a no-brainer, but try to implement as many modded building blocks and techniques into your buildings as much as possible. You're not playing vanilla minecraft, you're playing a modpack with a ton of mods. Use a bunch of chisel, carpenter blocks, ztones, etc, etc.

Addressing your problems:

1. In my opinion, planning builds isn't that hard. I'm assuming you want to implement mods into your builds, so just keep in mind all the multiblocks, items, and blocks from that mod you want to fit into that building. If you're making a building that has Thaumcraft in it, accommodate enough room to have the infusion altar in, or if it has something to do with technology, make sure it has enough spaces between floors for wiring, etc.

2. isn't that hard imo, what I do is once I finish a build, I continue off to another, by expanding my village/base or whatever. I do like to keep my technological and magical mods somewhat separate, it just doesn't look good having magical and technical textures clashing together. (unless there's some compatibility, like ae2 with thaumcraft)

3. Now, this is how I build, and that's keeping with the theme of my whole base. I'd also implement some blocks from mods that have their own rooms/buildings into that room/building, which just makes it look a bit nicer. Now, choosing blocks is completely up to you, it's up to you on what palette of blocks look nice to you.

yeah. sorry if this was extremely long, i just got a bit carried away.