I think boarding should generally be high risk and require a lot of marines (probably more than now) except for small ships, so that you mostly only bring marines along when you specifically want to capture a ship. To make this possible, you should be able to select 1 of the enemy ship as a capture target to greatly increase the chance of having a boarding opportunity. Perhaps doing so would also give you some sort of penalty, to simulate the fact that you and your captains are trying to "take this one alive".
What this sort of change would result in is that people would buy a lot of hopefully expensive marines, both in purchase cost and supply upkeep, then hunt down their intended capture target and take a large risk in exchange for a decent chance at capturing it. There would be a cost, a risk, and a payout. That makes it interesting and introduces an actual choice the player has to make. People not intending to capture anything in particular could carry no marines or very few (to replace their lost frigates for example).
Pre-patch, the situation was that you could easily carry a huge army of marines and capture everything given the chance, and you were given the chance often. That results in a steady extra income for the player which is definitely not needed right now as credits are already easy to get just by destroying ships.
Post-patch (currently), the situation is that carrying marines is very supply intensive and the rewards are rare, random and generally useless.