So, on the topic of modules, I think we want at least the following: general sciences lab, workshop, shuttlebay, and the deflector sensor analysis module if it's available - the first two are core to making a truly multipurpose vessel, the third is a basic function we can't really do without, and the last would be extremely useful for mapping weird spatial anomalies before the Curiosities come along afterward.
Additional, optional systems to choose between:
- biomedical lab - could be useful for more multipurpose reasons, as well as hopefully keeping the crew in shape over long voyages running into novel new diseases and shit. May or may not be worth taking, depending on how beefy the medical suite is (don't want to put the Curiosities out of work if we can avoid it, after all).
- bio-rated transporter - extremely convenient to have, but admittedly only 'better' than shuttles in a handful of edge cases (and usually edge cases have the transporters not work, rather than the shuttles); while an explorer is likely to encounter such edge cases at a statistically higher rate than other ships, there's still likely to be pretty fierce competition for module slots.
- secondary computer core - even with only a single lab, the explorer is likely to have enough to do in general that extra bandwidth is rarely going to go amiss.
- medium (or higher) cargo - honestly, this is a very low priority in my opinion; if I'm inferring right, it seems likely that Starfleet vessels come with the equivalent of a 'small' cargo bay (probably distributed throughout the ship in smaller chambers that are below our level of abstraction to see) sufficient for supplying themselves for normal operation. Medium or better would be good for longer-term voyages but ehhh?