Let me address points individually.
Admittedly, the glitches you found were more legitimate than I expected. Momduck was a joke that's just supposed to be silly and potentially amuse some people. Calling Momduck a glitch is about as founded as saying the boxes in the room are a tile error. Alternatively, you may be against psyduck adoption policies. Why would you? They have as much right to own a human as you do to own a Psyduck.
The other points are mostly legitimate things that aren't intentional, though. Yes, you can go south of Pallet Town after beating the Rival there. However, you don't HAVE to get the Pokedex as a result. Not having a Pokedex does absolutely nothing to this hack gameplay-wise (I worked with the code so 2nd and 3rd gen evolutions still work just fine), so the Pokedex quest only amounts to free Pokeballs and wild Pokemon. Frankly, the player should know how far away Cinnabar Island is, and if they want Pokeballs, they should also know how fast it is to get the parcel and suddenly have five free Pokeballs. It's still the world of Fire Red, so there's some background knowledge I expect the player to have.
Movement permission errors, I'll give you. My best guess is that I changed some tiles but forgot to add layers to the movement permissions and ended up never doing it, so things aren't working right. Whoops!
You are literally the first person I've seen complaining about the Aide. (Well, aside from a previous issue where the Aide would walk over a rock, but that's not there anymore.) If it makes you feel any better, think of him as having a desert condo somewhere. To catch up with you, he would be leaving his condo to block your path, and when he leaves in the direction that is not Pallet Town, he's going back to his condo. Why should he live in the same town as where he works? There are three buildings in pallet town, so he's logically more likely to live in the desert when you think about it!
The puddle water was an unintended consequence of two completely unrelated actions, and that was my mistake. Puddles have the same random encounters as surf water, so the obvious issues came up, and I never remembered to go back to every area with puddles to fix that.
The desert random encounters are just fine, and I have no idea what you mean about the surf water. Wild Pokemon are supposed to show up in the sand (though only certain patches of sand, since there's a wild Pokemon variety and a basic variety that are mixed in to spice things up). Regardless, the only thing I had to change when switching the water into sand was the movement permissions. Given that you don't surf in the sand, I think it's fair to assume I did that part correctly!
So basically, you're completely right. The game is lacking polish, but the two errors here where I agree with you (the movement permissions and the oh god overleveled psyducks) are some of the only mistakes in the game, if I recall correctly. Really, this isn't the hack you put in a contest, but more of something to show to people so they have fun. (Usually they do.)
Just take everything in stride and it really is a good hack, but if you get hung up on problems that don't matter much in the grand scheme of things and you'll hate it.
(Sorry if it sounds like I'm taking critiques of my hack as a personal attack on myself. I just make big posts in response to complaints so I can get my opinion across on everything that's said.)