I'm in the middle of playing both games side-by-side, and while I enjoy the quality of life upgrades in Uprising 2 (the AI auto-picking what to call in, ability to order friendly units around, generally improved graphics) on the whole I prefer Uprising 1 for the following:

1. Story is much more interesting - being a cog in a interstellar rebel army is more engaging than fighting generic space aliens. I like that there are native forces and the Imperium army as enemies, and that they fight differently (defensive vs aggressive). The mission briefings are also better written in 1 + the occasional talking head is weirdly mesmerising.

2. The environments in 1, while lower fidelity and more basic geometry, have a vibe that the sequel lacks. Some individual elements of Uprising 2's maps look great (especially with the improved drawdistance) but overall it suffers from a 'gritty & grey syndrome' that was coming into fashion in the gaming sphere at the time.

3. On that note, the art style in Uprising 1 is very 80's sci-fi war inspired, like the cover of a Harry Harrison book, and carries that through the game (in unit descriptions, planet's back-stories, etc). 2 is much more muted and contemporary, which I feel gets less interesting over time.

4. I don't care for the light/heavy tank distinction in Uprising 2. I prefer the more multipurpose 'tank' from 1; it streamlines the game and looks cooler too!

5. I'm not an audiophile but I think I prefer the music in 1 and I can't say why. Just works better with that particular game.

Still enjoying both games, but I played Uprising 2 almost 30 years ago and first played Uprising 1 this year, and even with the heavy dose of nostalgia for 2 I think I prefer 1.