Basically everything paraxade said. To emphasize, before starting ANYTHING at all, PLEASE just sit down, play with the game, do
some a crapton of research and understand the physics more. The tas is going to be absolutely terrible and unimpressive if you don't do so, and this is easily the most complex game in terms of mechanics.
Following the general route that the current record uses isn't too bad of an idea, but with TAS capabilities, going out of bounds will be much much more useful in general. OoB isn't used often in speedruns for prime 1 because it's really hard and risky to navigate and generally slow, but that isn't a problem for TAS. I believe itspersonnal said that, for example, going out of bounds in phendrana shorelines to get wave beam is faster than staying in bounds for example.
I think itspersonnal has a video of 2-pooling Omega Pirate but I'm not sure; he also messed around a lot with bunny-hopping mechanics so really, you should just poke him about a lot of the TAS things he's messed with. You should also poke petrie about his prime phase 1 TAS, I believe he has that somewhere on youtube.
I recommend reading through the metroid2002.com threads to learn more about the game and ask questions there, since a lot of knowledgeable people are there and willing to answer. I especially recommend reading this:
https://m2k2.taigaforum.com/post/random_research_topic.html
https://m2k2.taigaforum.com/post/2pool_metroid_prime.html
Also, here is a chart of every drop rate that Miles found in the game data:
https://docs.google.com/spreadsheet/ccc?key=0AoVqC1jrYPrhdGs4WmhUbUxvZUI1TV9WME15cXVyV1E#gid=8 ; he also found a lot of other things in the inner workings of the game so it's best to ask him a lot of things.
Skipping space jump and boost ball are completely out of the question for any%, they save far too much time to skip, especially space jump (which costs like 3 seconds to get in-game time and will probably save minutes in the long run).
The thing about fighting prime without thermal is that you have to aim blindly, which shouuldn't be a problem for TAS obviously, just annoying. Getting thermal visor barely costs time for in-game time (real-time it does because cutscenes) because you have to fall down the room anyways, which you can spend that time finishing most of the scans. I do recommend optimizing for in-game time as it makes the gameplay overall look faster, and it's the standard for the prime speedrunning community.
Finally a short outline about low% for metroid prime that I made a while ago (and includes 2+3 as well):
http://pastebin.com/BH7y00rV ; could be useful in just general learning about the game.
Good luck!
EDIT: Miles and Petrie also put together a damage chart at some point, not sure where the full one is, but I have this from something miles posted on gamefaqs a while ago:
Power Beam (uncharged): 1
Power Beam (fully charged): 25
Wave Beam (uncharged): 1 for each of the 3 waves
Wave Beam (fully charged): 20
Ice Beam (uncharged): 10
Ice Beam (fully charged): 30
Plasma Beam (uncharged): 6 (not counting the burn)
Plasma Beam (fully charged): 50
Missile: 15
Super Missile: 90
Ice Spreader: 75
Obviously ice spreader would not be collected in a TAS; it's collected in single-segment runs since it makes prime a lot easier and less RNG-heavy, and it costs very little time to get, but it doesn't actually save time if the fight is done optimally. (ice beam also does double damage on metroid prime phase 1 IIRC)
EDIT2: Might as well mention some techniques that parax left out that you should research on.
-Ghetto Jump - Height technique. Press against some slope to gain height. More information in miles's research thread i posted above.
-Bomb Space Jump (BSJ) - Height technique. Manipulate the camera such that when Samus bomb jumps, she gets an instant unmorph in 21/22 frames and can then jump as she's on ground. Read miles's research thread for more details
-HBJ/UBJ -
http://www.metroid2002.com/techniques_hbj_ubj.php
-Aether jumping - When OoB, when you walk from the side of aether and into the box of a room, you have a 3-frame window to jump out of it. This is the basic way to climb up rooms without using standable OoB spots. TAS can abuse this and dash out of it to traverse OoB very quickly, so I recommend messing with it (obviously not done in real runs because it's way too risky and difficult lol)