The way I see it is the lack of Autobot numbers was because the Bots were taking a pasting from the Cons at the time.

They had lost Cybertron. They may have tried retaking it, thus losing more guys. Really, the assault on Autobot City was more the Autobots last stand than anything else.

 

Decepticons already had Cybertron or at least most of it in Ssn 1. Autobot city was not a city, really. It was a power plant making energon. It wasn't their last stand. It was the way back. That's why the Autobots were going to earth. To get power so they could make a full scale assault on Cybertron and try and get back on the planet.

 

Why'd the Autobots lose in Autobot City?

Cause their toys weren't being sold anymore. That's all. They were written to lose for that reason.

 

there should have been a battle at the ark between the wreckers superion ,defensor and bruticus menasorand omega supreme with omega dieing in a two on one battle to the death with bruticus and menasor just barely limping away from the battle alive

 

Ok, he gives us a valid point here. Of the Autobots I counted, or know about from storyboards, I count:

1. Hot Rod
2. Kup
3. Huffer
4. Bluestreak
5. Sunstreaker (or a look-alike)
6. Hound (or a look-alike; helping Kup, "Sunstreaker", and Bluestreak with the barricade)
7. Perceptor
8. Ultra Magnus
9. Blurr
10. Springer
11. Arcee
12. Blaster
13. Eject
14. Rewind
15. Steeljaw
16. Ramhorn
17. Wheeljack
18. Windcharger
19. Smokescreen (storyboard only)
20. Mirage (off-camera, but storyboarded)
21. Sideswipe (storyboard only)
22. Grapple
23. Red Alert (storyboard only)

Of the Decepticon contingent (most of which were visible), I saw:

1. Megatron
2. Starscream
3. Scrapper
4. Bonecrusher
5. Long Haul
6. Hook
7. Scavenger
8. Mixmaster
9. Soundwave
10. Rumble
11. Frenzy
12. Ravage
13. Ratbat
14. Laserbeak (only shows up on the return trip)
15. Thundercracker
16. Skywarp
17. Dirge
18. Ramjet
19. Thrust
20. Blitzwing
21. Astrotrain
22. Kickback
23. Shrapnel
24. Bombshell
    (I allow for the possibility for Insecticon clones.)

Pretty much every Decepticon manufactured for the 1985 line, plus Ratbat should have been present, excluding possibly Buzzsaw, Reflector, and the Deluxe Insecticons (who, again, would have had Insecticon clones as stand-ins).
That being said, there are dozens of Autobots who could have been here, if only they'd been created by the time of the film's production! In an Autobot City, it'd only be natural to have the Protectobots, if not the Aerialbots (for the sole purpose of air defense). Wrecker favorites Whirl and Roadbuster would have been good additions, as would have been Omega Supreme (who was likely serving in his role as guardian of Autobot Headquarters/The Ark). Metroplex himself wasn't created until after all the work was done. This is why the writers of the Dreamwave (or was it IDW?) movie adaptation and the writers of Transformers Season 3 added hastily-conceived reasons for the other Autobot heavy hitters' absence. (In Metroplex's case, his transformation cog was damaged during the invasion, so he got no further than battle station mode, even with manual assistance.) Also, being a city, I'd suspect many of the Autobots and humans quartered there were civilians and non-combatants. On the Decepticon front, also notice that Menasor, Bruticus, Octane, and the Battlechargers weren't present.

The Decepticons fared so well due to an element of surprise (in spite of Hot Rod), and being on the offensive, they were more combat-ready (fully fueled, with full armament and ammunition) at the start of the battle. If you storm an enemy camp, it's probably best to do it when their guard is down (i.e., most of them are asleep, slacking off, drunk, etc.). I hate to say it, but especially with Hot Rod's actions, the Battle of Autobot City was the Autobots' 9/11.
-- Cybertronian.
P.S.: I'd lose count if I tried to imagine every Autobot produced by our 2005 who could have been present then! Where were the Railrobots (Railspike, Rapid Run, & Midnight Express), or Landfill, Quickmix, and Scoop? Or Crosshairs, Sureshot, Hardhead, Skyfire, Groundbreaker, Mach Alert, and Hot House?

 

In the storyboards, the Dinobots give Devastator a much bigger fight, with Swoop actually doing something. The reason Devastator isn't shown later is beacuse after he wrenches that wall open, he is forced to seperate by shots from Ultra Magnus, Sideswipe, and I think Tracks.
Red Alert is getting trounced (or chased, I forget) by Megatron when Prime shows up (to say "One shall stand, one shall fall"). After Megatron's response, Prime is seen rising up after giving a recovering Dirge (who tried to jump him from behind) a refresher course in WWE tactics.

 

I could suscribe to this line of thinking. It certainly makes sense to me.

Now see, this makes me wish that alot of scenes were not cut out of the movie so that if anything else the movie could've been longer.