I will be making a thread at some point towards the end of HC for discussion on good/bad/thoughts on how HC went to help revise the rules if a second season is in order, or to help the next event if the scene moves a different direction. This is naturally one of the things that would come up.
One potential way of handling it would be that one team locks one ship, the other team locks their ships, then the first team locks their final ship.
I think part of the reason pyramidions and junkers are the most popular ships is simply due to them being pretty good all-arounders. You can take them into any match and have a pretty good shot at not being "hard" countered. Other ships face more counters, making it a greater risk to take them into a lobby where your opponent will see it and potentially switch to counter it. A system for locking loadouts would potentially help more ships flourish in competitive, though recent days have at the very least seen more goldfish put to good use in HC even without hardline rules.
Always interesting to hear new ideas. This is a tough subject because no matter what, either at least one ship will get final choice or teams will be blind (which leads to generic builds). Luckily, so far HC seems to have seen pretty good variety without too much posturing and countering in lobbies.