I played through the whole game with this randomizer, and it's relatively well done.
Of course, there were some things I thought of whilst playing it that could add to the gameplay and randomness of the experience, such as:

1. Well, randomized EXP per weapon. (preferably like a random number of 1-100, don't want to make a level 1 polar star require like 999 EXP.) (also the highest EXP of a normal weapon is ~60 EXP anyway, wouldn't want it too unbalanced with vanilla.
2. Make all text just go fast, or skip cutscenes. (Basically setting all text boxes to have an instant text display command on them, although, some additional tinkering of the text boxes may be required because in my experience, doing that seemed to break how the text is displayed.)
3. Randomized text for each individual NPC, just because because that could end up being extremely silly. (although, that's a lot of text.)
4. Logic for randomized story items, so that you can still find story items in their respective areas or otherwise, just in obtainable places if you are able to get there with the equipment given beforehand.  (e.g. : Santa's key could be in the "Execution Chamber", the tiny room with the presses and life capsule, if and only if you have a machine gun.)

Shuffling key items would definitely add a lot of depth to the gameplay, and skipping cutscenes would be really good.

What about letting the player teleport to Egg Corridor, Bushlands and Sand Zone from the start?