Most of the problems I had with BMZ are just hold-overs from the original that they should have cleaned up. It still the same cheap hits from leaps of faith, the same crappy stutter in the aiming (although you can just hold R to aim diagonally now), the same frustrating difficulty in getting Jason to reliably aim at an angle, and the same finicky controls when driving up walls and around corners. The major one to fix would have been SOPHIA's weird, floaty jumps but they left those in. You get used to it as you play but the platforming just never feels right because of it.
Some of the new additions aren't bad, but they just don't really hit. There are a lot more upgrades but most of them are useless or are used for one-time issues. Jason gets some land mines that serve no purpose and flash bombs that are only ever needed for maybe three dark dungeons. SOPHIA gets some chargeable shots that aren't worth it and subweapons like a pillar of electricity that has no viable combat use. Several of the items you'll use once for a puzzle or are needed for that area's boss and then they just sit there cluttering your inventory. They're acceptable at best rewards for exploring but they're really not hard to find, outside of at one point, you can drive through a wall of lava that looks like a solid wall while the rest of the lava in the stage hurts you. That's just dumb.
Without spoiling anything, there are some changes to the bosses, mostly for the better. Some were removed, some were added, one was moved from a Jason fight to a SOPHIA fight (it took me a while to even realize they were supposed to be the same boss), and lots of bosses are just combat arenas against small enemies that spawn in (and they're always a bore). The boss at the end of the normal game is pretty awful though. Its moveset basically consists of: it's a lot bigger than you, it's a lot faster than you, and it does contact damage. It felt like luck that I beat it on my fifth try. I didn't do anything different from the previous tries, I just got lucky that the boss didn't try to walk into me as much. The extra area for getting 100% of the items is also lousy. It doesn't feel much like a level, it's just a bunch of random things thrown together with a lot of repeated bosses. But then the real final boss is actually pretty cool. You fight it as both Jason and SOPHIA, so it's a nice change of pace. It would have been awesome to see that fleshed out a bit more and having you switch between the two in the actual fight, but it was still pretty different so it made for a good finale.
I beat the game in around 6 hours (the in-game clock continues to run even when you're paused so I'm not sure what the actual time is) and that was taking it slow to backtrack and explore a lot. But for $10, that's a pretty good length and it would probably feel like it was dragging on if it was any longer. The updates most certainly make the game easier, but they also make it far, far more enjoyable than the original. Blaster Master Zero is nostalgia done right, especially compared to games like that Wayforward Duck Tales game that got it all wrong. It tampered with what I remembered, changed the music for the worse, changed the levels, and shoehorned in constant story segments that broke the flow of the game. BMZ preserves what the game was in my head and made it a bit more fun. It instantly starts off with one of the NES's greatest pieces of music, the changes make the game more playable, and while they added in story, it's contained to specific moments so it doesn't interrupt the gameplay. If you have any fond memories of the original or are looking for a nice, simple exploration game with some anime science frogs, Blaster Master Zero is worth a play.