You ever tried to keep 15 lasers locked at once while hopping on one leg and praying to the ion gods that your ablation target will last a few more days?

Jokes aside, do you have a particular measurement in mind, or just interested in building it cause you can?
I would speculate that there's just no application for laser cooled molecular ions in a penning trap. Parity searches in molecular ions are hard because you need a rotating E-field to Stark shift/polarize the opposite parity states (like the HfF+/ThF+ experiments). I don't think you can make a rotating E-field in a Penning trap (watch someone make a fool of me for saying this). As far as quantum simulation/computing, molecular ions are worse than atomic ions or neutral molecules. Neutral molecules have big dipole interactions over short distances, but molecular ions have long-range coulomb interactions that prevent ions from getting close enough for dipole-dipole stuff to happen. Atomic ions interact strongly via coulomb forces just like molecular ions, but the atomic ions are waaaay easier to repump and just cleaner systems overall (in molecules (esp. heavy ones), some transition "rules" are more like "transition suggestions").Yep!In the proposal paper I linked, the first round of cooling is done by resistive cooling in the penning trap. So yes, there is no need to directly excite the molecule at all!You're right, it will. In that proposal paper I linked, they do the sympathetic cooling + quantum logic in a different trap configuration than they do the spin precession. In short, they bring the two much closer to do logic, than they pull them apart before doing the precision measurement.Yep, you're right. It's much easier to use DC and/or RF E and B fields to control ions than it is to MOT them. The only people I know who tried to MOT ions attempted it as a flex.