If you compare demos on ECS and AGA... yes, there is a huge difference. There aren't a whole lot of AGA only games but they do look real nice compared to the ECS ones. WorkBench can be set up fancier with AGA. The main graphics improvement shows in demos and graphics apps though.
AGA machines have other nice things though, like Zorro III.
Once you use an AGA machine you won't want to be limited to ECS... but ECS can do many cool things.