I agree. The SOPHIA sections were great, but the top-down Jason-only sections really play like hot garbage(at least to this jaded 30-something gamer). I tolerated these areas when I was younger (with the aid of my trusty Nintendo Power dungeon maps), but in this most recent play through, I found myself just wanting to leap frog this areas and get back to the tank.
In the top-down sections, it seemed as if the game was designed to require the player to memorize enemy positions and patterns in order to successfully pass without getting hit. When you lose gun power every time you are hit, this is a drag. It's an interesting concept, but I think it mostly works to the game's detriment due to some of the design decisions. Even the mid-tier gun power-ups are weird; I found that some of the levels actually put you at a greater disadvantage, especially when the bullets start looping in wide arcs and end when they land on an obstruction. Even if the game dropped gun powerups more frequently, this wouldn't be as much of an issue.
Also, I always remember being disappointed that Jason's gun power-ups didn't somehow translate to the side scrolling sections where you control Jason. This would have been useful for the entirety of Area 5 (the underwater sections).
Despite it's difficulty, my favorite section of the game is also one of my most feared: Area 5. I love the music in this stage; it's relatively serene when compared to the rest of the soundtrack, but since you spend most of your time separated from the tank, it represents one of the most vulnerable and dangerous points in the game. I love that sub power-up, though; after that is acquired, Area 5, is one of my favorite sections of any game ever. I always felt like I had accomplished something after passing that entire section of the game, and I felt like the tank-sub powerup was fun and fairly empowering.
In general, I'm not sure I can say anything else that hasn't already been stated here or will be stated on the podcast. Blaster Master is one of my favorite games of all time. I saved for this as a kid, owned it, and played the ever-loving crap out of it. I loved Sunsoft game sountracks in general, but Blaster Master has one of the best game soundtracks of all time, let alone on the NES. I kind of wish there had been worthy successors in the series that matched the best parts of the original.
As an aside, I enjoyed Blaster Master: Overdrive well enough, but I was mostly sad that the music remixes did not hold a candle to the originals.