Man, you are full of bad opinions.
Guardian Heroes' 3-plane system should have been aped by every 2D beat-em-up that followed it. It allows for inputs and aerial combat with the type of complexity you normally only find in 2D fighters, and it created a template for competent 4-player traditional fighters. (The game even clearly shares a legacy with their Yu Yu Hakusho and Bleach fighting games.)
The XBLA version went to tremendous lengths towards making the versus mode at least borderline respectable for balance, too.
Guardian Heroes' three-plane system should have been forgotten and buried, and never heard from again... multiple planes in this kind of game was an awful idea. Multiple planes are just as bad of a failure in fighting games, too -- the first seven Fatal Fury games have that, and it's annoying and is one of the factors in why I don't like any of them. SNK's fighting games are usually great... except for those. At least Garou finally ditched the stupid two-plane thing, and was much, MUCH better off for it!
As for moves, you don't need a 2d plane to have fighting game-style moves in a beat 'em up. See Final Fight 3 for example.
Multiple planes do work in platformers, though. Virtual Boy Wario Land and Donkey Kong Country Returns are absolutely fantastic games.
I don't think having seven weapons in Silvergun is a bad thing. Having more options at any given moment is generally good.
It's not just that you have seven weapons (it's seven, not six? Okay.), it's that you have them all, at the same time, and you're expected to use all of them. That's a pretty seriously weird concept for a shmup, and has to require a good-sized learning curve. And as I said, I'm not convinced it was a good idea anyway.
That said, IIRC the biggest thing people take issue with that game is tying your weapons' strength into the scoring system, which can leave you severely underpowered at the end-game if you're not playing the game "correctly". (Less of an issue for the Saturn Mode, since your weapons' levels are saved between playthroughs...)
It does that? Score determines weapon strength? I didn't know that, that sounds horrible!
I have the STV version and it's actually just 3 buttons with combinations to get all the weapons. It's much quicker to switch weapons that way and you can remap to ABX on a Saturn/360 controller to emulate this.
How would three buttons with combinations be faster than separate buttons for each weapon?