• Morph Ball, I don't count as a power up, because you practically start with it.
• Spider ball is used to gain access, but it's not lame, because you can access just about anywhere with just spider ball and a lot of patience.
• Jump ball is just a convenience. Again, with enough patience, you can mostly do without it.
• Space jump can be used to bypass enemies, or to move arround in combat; it's much more than a simple access mechanism.
• Screw attack isn't even used to gain access in Metroid II. Screw attack is just that: an attack. Since it made you invulnerable in Metroid II, it was also useful for retreat.
• Grapple beam, again, has combat usefullness. Anywhere you can get with grapple beam, you could also get with space jump, but you can't hang off walls and shoot with space jump.
• X-ray visor doesn't gain you access to anywhere; if you already know what's there, you can get it just fine without.

On the other hand...

• Speed boost, you might argue, can also be used to bypass enemies, but the fact is that it's only true of areas that were specifically designed for you to be able to use it that way. The ammount of warmup time is so great that you really can't effectively use it except where it was designed into the level, which relegates it to lame access block.
• Super missles. They do three times the damage of normal missles. And you can hold like 20. Right. The sole purpose is an excuse not to be able to access new areas.
• Super bombs. They kill everything in sight -- if it was garbage that you could kill in one shot from your beam. Again, only truely usefull for area access and scripted sequences.

At least I didn't feel "boxed in". And no, you don't just go deeper; you actually fight the last boss rather close to the surface. The tunnels between areas felt a lot more organic than in Super Metroid. In Super Metroid, it seemed like they opened most areas up into a box shape just because it was a box on the map.