If you're concerned about "waiting a long amount of clock time" for the passive regen, I came up with an alternate idea.
The aura repairs only shields. Out of combat, shields regenerate rather quickly. In combat, shields don't normally regenerate. This aura could bypass that rule and allow some amount of shield recovery during a firefight. Example:
A shield repairing pulse that goes out every 3 seconds restoring 100 (per rank) shields to all friendly things within (range determined by rank, similar to it's repair range).
The pulse would repair shields EVEN IF ACTIVELY TAKING FIRE.
An ability like that wouldn't be true multi repair but it would make this the "my fleet lives longer" ark without a doubt.
We'd having to make sure bugs didn't occur with things like armor ships (0 shield cap getting shields = possible problems) and so forth. I don't want it % based because it'd break golems, I think a number similar to my suggestion above is probably fair.
Another option would be to have the Ark generate "points" over time that amount to free repairs for nearby things, up to a cap determined by rank of ark. It would then expend those points repairing the things. This would leave the "optimal playstyle" issue in effect...
But what if the Ark experience points (or w/e they are called that you use for upgrading arks along with research) ARE the free area repair points? It might make ranking up the orchid harder, but since I tend towards having a fair number of points sitting around I doubt it would be a large negative impact... just have to hang back with the Ark away from the fleet combat to get the points to rank up with is all.
The least interesting option would be +(rank*X) armor aura. Not exploitable long term, notable survival buff, non game breaking, plays alongside theme. Not going to lie, I think it's good but not "flashy" enough. Arks are a centerpeice, they need to be flashy in some way.
Of the ideas I listed, I like the first as an alternative to multi repair best, personally. The third has the potential to be the most powerful, used cleverly.
One other point: those who wait long times to be optimal must be careful, for we fail to realize we're at the metal cap and could be adding engineers.