I cannot in a nice and concise paragraph say why full legal stage striking (FLSS) is the only way to find the true neutral of every match-up so I am going to start out by talking about what makes a character better than another character.
In brawl we get the joy (or curse, however you want to look at it) of having stages which affect gameplay and character balance. As a result every single match on every single stage is different. Diddy vs Falco (DvF) on Battlefield is a different match-up from DvF on Smashvile which a different match-up from DvF on Delfino.
Every single character match-up has multiple sub-match-ups contained within it. The result of this is that we are not able to know which player is truly better unless we were to play a match on every single legal stage and award the victory to the player who won the majority. The conclusion from this is that if character A is better on the majority of stages than the opposing character B, character A is better character.
Playing out a match on every single stage however is exceedingly impractical due to time constraints and forces us to look for a way to simplify the process. To do this we must create a system which emulates the effect of playing a match on every single stage in the game without taking an extraordinary amount of time. For the system to have this result the system would need to cause match-ups that favor characters who win the majority to continue to have the advantage.
To find a system which does this it only takes a bit of simple logic. If character A is is better on a majority of stages than character B having both characters strike a number of stages equal to the total legal stage roster minus 1. This results in both characters being an equal number of stages away from their best stage and as a result they reach what is know as the median of bias.
FLSS is designed to reach the median of bias and as a result causes characters who are better on a majority of stages to be given an advantage. This incidentally causes characters who are good on a select few stages but poor overall to be given significantly less advantage then they are now, ice climbers being the most visible example. On the flipside characters who excel on multiple stages such as Wario, game and watch, and Metaknight will be given the advantage they rightfully deserve for being superior characters.
Now that the general theory and logic behind FLSS has been stated, I will continue on to address each of Alpha Zealots individual.
-Makes both players only play on their 5/6 best (really though, worst) stage of which neither will be entirely comfortable, why start a match on a stage neither player would actually prefer to play on?
There is nothing wrong with players playing on the stage they have a "meh" reaction to if the stage is fair.
-More importantly, over the course of several thousand matches, I doubt several stages would be used even a single time, in which case striking them was simply a formality and a waste of time.
Those stages may not be used but by removing them entirely you will be causing a skew in the natural match-up between two characters and arbitrarily causing match-ups to change.
-The idea that full stage striking somehow leads to the most "neutral" stage for the first game for any two given characters can be no more proven true than that of 5/7/9.
Read the argument above. If your intention of a starter list is to represent a match in the most fair way possible then FLSS is in fact the most effective manor.
-Yes, lets make already complicated Smash rules and already long/drawn out match beginning routines take EVEN LONGER for almost no real gain.
Telling players to alternate stage strikes is really not that complicated.
The gain is that we are preserving the game's inherent balance and are allowing good characters to be good and bad characters to be bad. It avoids the creation of double standards, and is much more logically sound than the current system.
Metaknight is only intolerable on his two best stages, and is a nuisance on his less powerful counterpicks. The stage he will be taking to like you said will be his 6th or 7th best stage which in the majority of situations will be something already present on a 7 stage starter list.
I have other priority at the moment so I will not be able to respond to arguments about this post for about an hour or so but I will be back shortly.