In reverse order, I don't do any automated eroding, so I can't help there. When I start with a Fractal Terrains world I'll look for improbable basins and lift and/or smooth til they're more plausible. I tend to isolate FT-genned rivers on their own layer and use them as suggestions, wiggling my own watercourses into place including minor water-gap type editing to figuratively drain closed basins .
Your mountain ranges do show improvement over an as-genned FT planet. They still have about the same degree of roughness - maybe you could blunt some of the smaller interior ranges, turning them from recent uplift/ collision events to more Appalachian/ Ozark equivalents. Since you're willing to do some tectonics maybe with details you can make a few massive interior ranges to be ongoing plate collision situations (Himalayas). Since you show sea floor detail, try manually digging sharp slots of subduction trenches just offshore of some of the nearly-coastal ranges. Add a few more conical peaks and you'll be representing subduction volcanic belts (earth's Pacific ring of fire). You could manually drop in one or more rift valleys to show divergence.
I'm not sure why you want to prevent massive plains -- is it that you want to avoid having them look heavily eroded like your first pic? An FT limitation is generating the whole planet with the same fractal degree. Manually adding big swaths of plains, steppes, and plateaus is a necessity. If you don't need to keep the sea floor detail, consider the trick of expanding continental shelves, then dropping sea level in some places to get coastal plains.
Take a look at your coasts worldwide. See how all have that similar degree of roughness? Look at Earth and note wide swaths of coastline by that are smoothly sculpted into barrier islands, sandy beaches, swampland.
It can be a pain doing all the manual editing, but the results can be way better than defaults produce. I wish I had the persistence to get into applying Wilbur to planets -- you're ahead of me there! Looks to me like you have a good start - I'm looking forward to seeing it progress.
Oh, and thanks for jumping right in with a substantive contribution - maps in one's first post is worth a smidgen of rep!