Throwing some more random ideas around, I think one serious issue of the Prequels is the lack of design consistency. I do not mean only visual design and aesthetics, as Episode 1 clearly looks like the odd one (although certainly the best one, IMHO) but how consistent the universe is. Of all the designs to appear in the Prequels, the only one that appears in the entire trilogy are the B-1 battle droids, and the Neimodians. That's it.
Now, take the Original Trilogy. You have a great diversity of designs but coherence too. Ships and vehicles are characters in themselves and clearly help reinforce the overall feeling of the different factions. You can easily distinguish who's vehicle is on screen, and it helps set a mood and tone to the scene. The OT had several designs appear in the entire trilogy with a lot of screen time:
- Star Destroyer;
- Millenium Falcon
- TIE Fighter
- X-Wing
In the entire trilogy with more limited screen time:
- Blockade Runner
- Y-Wing
- Super Star Destroyer
- Rebel Frigate
Additionally, there were many designs that appeared in two movies, or had enough visual coherence to be immediately identifiable (Rebel Runner / Gunship, TIE Bomber / Interceptor, etc.).
What does the prequel have, appearing at least in two movies, disregarding the horrible battle droids (admittedly, there's enough footage of these guys to edit them into decent adversaries)? The Trade Federation "donut"ship, at least a memorable design, the N-1 and... eh... ?
Te Confederacy looks like a toy store, not an actual military faction. At least not one that is coherent enough visually so as to be easily identifiable as an adversary in a movie.
We need more ships to actually be characters in the Prequels just like the Falcon was in the battle against the Empire. I'd really like to see some of the Confederacy ships, like Grievous' Invisible Hand cruiser, introduced as early as Episode 1 and other, like the AAT tank or STAP speeder persisting throughout.
Not to mention a central ship acting in the fashion of the Falcon. The Prequels desperately need that. For a movie called Star Wars there was most definitely not enough space, even as a setting, much less space combat action, in Ep. 1 - 3.
PS. Excuse me horrible English, not my native language and I'm dead tired as I write this. I hope it is comprehensible ?