It's pretty well agreed that the bots2 system didn't work because it gave too much advantage to high level bots in clans. By 2010, your clan had to be stacked with level 150+ bots just to compete.
The current bots4 system went in the opposite direction and took level out of the equation completely.
My current thoughts are that a balance would be best. Level should factor in somewhat, just not to the point where it's impossible to compete at low levels. I've actually already worked out how I plan to do this and it will be included in the upcoming clan/energy system update. It's not a formula change fyi.