Since most people seemed to ignore my rather lengthy reply, I thought I'd cut to the more interesting half of my post, and make it a discussion unto itself.
Thanks for posting! I’ve been a little backlogged with Sam & Max stuff, but I was really happy to read your thoughts. I hope to write full replies to each of your points soon, but if you subscribe to the theory that actions speak louder words, then the first episode of Sam & Max might be an even louder reply. I’m interested to hear if Sam & Max managed to evade these pitfalls any better, and where it could still use improvement.
But for the short answer, I think you make many very good points. I've experienced all the problems you mentioned, and I too want to correct them. In Sam & Max, we didn’t choose to address the problems in quite the same ways you proposed, but we certainly worked to make the puzzle design more consistent and to maintain a pleasing pace. I hope it paid off, but if not, let us know and we'll keep working at it!