First up, this is an excellent suggestion. Boarding is definitely too much of an easy decision and is, for the most part, pretty unrewarding unless there's a specific ship involved.
What follows is just a brief suggestion on how to make the actual boarding phase a little more interesting. Feel free to ignore.
Why not have boarding also be a bit interactive. Like guiding your green dots throughout a blue ship and righting red dots along the way.
I do think that there's an opportunity here for a mini-game. There are two basic problems though,
1. The AI has to be able to respond to it, so it must be simple or require little to no AI resources.
2. It has to be entertaining and short enough, regardless of the sizes of the ships involved, that auto-resolve is not the default choice.
One thing that comes to mind is something similar to the Final Fantasy 7 boarding scenario. For those unaware of the game (or have simply forgotten this part of it) it essentially asks you to prioritize the areas you want to attack and defend and then resolves accordingly.
Say there are five areas: 1. Command centre, 2. Initial boarding area, 3. Engines, 4. Armoury, 5. Support equipment.
You assign each area a priority from 1-5 and hit resolve. At this point, a count-down clock begins on each section with the time displayed indicative of how long before the crew there sabotages the ship beyond repair with loss of all marines on board and/or damage to the boarding ship. The count-down clock would vary per section in response to the priority the AI put on the area. How quickly your marines moved to an area would depend on marine skill, any officer/skill bonuses and the marine-crew ratio.
You could make it more complicated by changing the damage each area 'lost' does to the ship (eg losing the Armoury might increase enemy crew effectiveness vs. your marines) but that's probably unnecessary.
At any rate, the idea here is largely to add a bit of excitement and strategy, however limited, to the boarding process. At the moment it's little more than a case of bringing overwhelming numbers and I don't feel that the suggestion as is goes far enough into offering alternatives. It would also get around some of the issues that cropped up relating to the difficulty displayed. At the end of it, the player would know exactly why he lost the boarding action - the AI decided to sabotage the ship using explosives from the Armoury while the player's marines went prancing around the Command centre. It wouldn't just be because the game just rolled a 1 on his 99/100 chance to capture the ship.