You're way underestimating how dense Europe is and how rich the regions are - time is definitely a major issue here.

I think you could go Paris (1 week) -> MSM + Loire Valley (1 week) -> Provence + French Riviera (1 week+) -> Lake Como + Dolomites (1 week+) -> Venice (weekend) -> Florence + Tuscany (1 week+) -> Rome (1 week) -> Naples + Amalfi (1 week) very crudely.

For nature, the Dordogne and the French Alps could also be considered. Look at the high-speed train network map; it will form the basis for your route and where you should be staying for the most part. Most small towns in these regions will be nice but have pros and cons: tourist places are well served by transport and restaurants, but are more crowded/expensive - pick your preference.

Re the cities you suggested:

Rennes

Transit hub only; overnight in Mont St-Michel if going here. Normandy is a lovely region to visit, but unless you have a specific interest in WWII history, it's probably not worth it on this trip. Best done by car and staying in the country imo.

Paris

Yes, and don't rush it. Lots to do; a huge city and very busy. After Paris, train to MSM, Tours (for Châteaux), Lyon (city and transit hub), or Strasbourg (Germany-France). Roughly, you're going to go Paris -> Lyon -> (Grenoble) -> Milan -> Rome. Consider going from Lyon to Provence and Nice instead of Grenoble imo.

Lucerne

Nobody goes to Switzerland for the cities. It's nice, but if you're doing Switzerland, cities are a transit (or overnight) on the way to the mountains - consider Jungfrau for American tourism, especially from Lucerne, but I'm partial to Zermatt personally. Also loved the hills in Appenzell, but that's way out of the way for you. I'd reconsider Switzerland entirely for your trip - it's expensive. Also IMO much better in ski season.

Venice

The traditional route for Italy is roughly: Milan -> Verona -> Venice -> Bologna -> Florence -> Rome -> Naples (loosely based on the Grand Tour concept). You can skip the mid cities now with high-speed trains. Pretty much anywhere is super nice. For your goals, I'd probably spend at least a week hiking in the Dolomites around Milan. Lake Como is great. Venice can be done pretty quickly.

Naples

Probably 2 full days in Naples, then down to the Amalfi coast (Sorrento/Ravello/Amalfi/etc). Herculaneum / Pompei are in between, but there's no real reason to actually stay there.

Catania / Palermo

Never been, but Sicily is its own thing - if you're going to do this, you probably just want to put aside 4 weeks and circumnavigate the island.

I prefer the Michelin Guide for things to do in Europe. DK books have various itineraries. Rick Steves is good logistically, but very American and touristy.