The biggest (and really only major) difference between the two is ethanol content.
Ethanol is one of several (and the most popular, due to cost) "oxygenating" additives added to automotive gasoline to make it run cleaner. The engine itself absolutely does not care whether it is burning ethanol or not, outside of a couple percent horsepower difference. The problem most aircraft have with ethanol is that our fuel systems are not built to tolerate it. Most aircraft have natural rubber components in the fuel system somewhere betweeen fuel tank caps and intake manifold (fuel tank cap seals, fuel tank bladders, fuel sump drains, fuel hoses, fuel pump diaphragms, gaskets, possibly others) that will not react well to ethanol - they get soft, swell up, crack and leak. 100LL contains no ethanol and thus does not suffer from such issues. True "Mogas" contains no ethanol - it is low-90's octane fuel without ethanol. Both are safe to use in aircraft with STC's for such, or specifically built with tolerance to ethanol. "Pump gas", or regular gasoline that you would buy at the local conveniece store for you car, may or may not (most likely DOES) contain ethanol, which will eat away at your rubber seals and will cause you problems (quite possibly catastrophic ones) later on, around 50-100 hours after you start using it. To run pump gas, you have to "harden" your entire fuel system against ethanol.
Ethanol is not the devil - but it is the devils handmaiden. Where you find it, you must guard against it. You must be ABSOLUTELY SURE - and experimental aviation is one of the few spots where this is possible - that your ENTIRE fuel system, from fuel tank cap to intake manifold, is free of natural rubber compounds to be able to run random pump gas successfully (assuming your engine compression ratio allows it with adequate detonation margin).
Let me emphasize it to be clear - if you do not hold a piece of paper from the gum'int saying that you are authorized to do so, then it is your own responsibility to make sure it is SAFE to do so and to prove to the FAA to their satisfaction to give you an airworthiness certificate. Experimental aviation allows us to choose our own weapons with which to wage war, so we have some leeway about how we go about it. We can use the standard off-the-shelf items for our fuel system, which requires us to run 100LL. We can modify that fuel system somewhat with STC-approved components that allow us to run mogas (low-90's fuel without ethanol). In the experimental world we can also toss the regulations out the window entirely and make up our own fuel system (dangerous without knowledge, quite fruitful if you pay attention) that can run any available fuel from liquefied hydrogen to coal. HOWEVER - if we choose to toss those regulations out and built our own fuel system, we have to face head-on the demons that caused those regulations to be in place - which means firm knowledge and facts instead of hearsay and rumor.
Yes, I know how to build one of these fuel systems and I have one. No, I'm not going to tell you how to do it. Yes, it is possible. No, it's not expensive or time-consuming. You just have to know what you are doing, what materials to choose, and no it's not difficult if you are willing to do a little basic chemistry research. No, there is not anybody else that's willing to do it for you - because we would be sued about a half-nanosecond after somebody screwed up and made a smoking hole in the ground. If you want to be safe, then run 100LL. If you want to be smart and efficient, then you need to be self-educated.
This is as far behind the curtain as you get to look - until you choose to believe...
