I like the Safari Zone, because it's something a bit different after hours of battles. It also provides a bit of an excuse for having exotic or rare Pokémon wandering around.
The Great Marsh itself was just another Safari Zone, albeit with a different setting. The deep mud spots were just a puzzle element to it, like needing Surf to access all areas of Kanto's Safari Zone, and shouldn't define it. The only thing new was the randomising of some Pokémon, which is a good thing (particularly as the binoculars show you which Pokémon are available).
I haven't used the Johto Safari Zone, but I think the area jigsaw thing is a horrible idea. These are huge chunks of land, and you're just moving them around on a whim? No thanks. While I do like the idea of having a water area or a desert area or a rocky area, I really don't like the mix-n-match feature. Just put them all in the same (huge) map, or a few separate maps with shuttles running between them. The blocks thing (putting random objects in places to attract certain species) is also stupid, if only because they're really random objects. The PokéBlock feeder was fine enough, but could still be expanded on slightly. I think the only change in HGSS I liked was the removal of the limited steps.
For all the changes made to the Safari areas, nothing has been done to the battles themselves. I would have thought that bait (which you throw during battle) could be expanded upon, at least - Hoenn did do this a bit, but that improvement disappeared silently. What I imagine is that there are several kinds of bait, and you can only carry a limited number of it so you'd need to go back to the entrance every so often to restock. Basic bait is free, but other kinds cost a small amount of money.
Maybe even have a few more items usable during a Safari battle, such as the Pokéflute (lowers flee rate) or watering can (makes species weak to water more easy to capture).
Maybe overhaul the Safari battle mechanics to include more than two variables (ease of capture and likelihood of fleeing) - perhaps include evasion too.