Slowing your training facilities

[Suicide Junkie]

The main problem, as I think you noted, was that each planet gets the best rate over all facilities AND the best max over all facilities.

The only way to prevent someone from combining a low-max/high-rate with a high-max/low-rate to get a high/high planet is to force one facility per planet.

You can also do it with ships/bases...
For training abilities, each ship/base acts as a separate planet.
If you make the costs of the high-maximum components very high, then players will only be able to afford one or two.
The lower ones would be cheaper, and more could be built and maintained...
If each base had a rate of 1, they would add, so up to the "cheap" level training, the player would have lots, and it would proceed fast.
Beyond that, only the expensive base would be able to contribute additional training points, and the rate of experience gathering would slow...