The longer serials can work based off what I've seen so far (The 6 episode Genesis of the Daleks from the 4th Doctor's run was a good 6 part story), and I'm not against them in general, its just that Doctor Who and the Silurians felt like it would have benefited from being shorter. I want to get to Inferno, though, and I don't think I'll skip The Ambassadors of Death. I think I'll just break up my watching with continuing the 4th Doctor serials (with The Deadly Assassin) or 2nd Doctor stuff. That way, I don't get burned out on Pertwee's super long stories in his first season, and I continue watching more stuff. I think rotating Doctors will help with any long stories and generally be an interesting way of watching more classic who. That doesn't mean I'll stick to it, but its the plan right now.
Just make sure you watch the Peladon stories in the right order, as they won't make sense if you don't (both are Pertwee era; the first has Jo as the Doctor's Companion, the second has Sarah, and takes place a few decades later from Peladon's pov).