If you maxed out 3 of the 4 possible upgrades then your level 7,8, or 9 capital ship has only ONE possible upgrade path. It should automatically "select" that upgrade as soon as the ship levels regardless if you have auto-level enabled or not (since there is no user choice, its just a matter of "the faster you click it, the faster it becomes more powerful".

And this goes against the whole paradigm of the game where its about strategy, not who clicks the fastest.

This is a pretty minor thing, but it would be a nice touch.

EDIT: you know, I am almost tempted to suggest that at 10th level the capital ship will purchase all available upgrades for the poor fool who doesn't know he can level capital ships and yet still manages to get one to level 10...

Or I guess it COULD be useful if you did level, but didn't notice it reaching level 9 and you have two unspent points and two separate unmaxed abilities (the two seperate unmaxed abilities only matter if the suggestion I made above is implemented... if it is then it will auto level as long as there is only one unmaxed ability anyways...)