The canon evidence on how ships are captured seems unclear. However, from a gameplay perspective I think ion cannons are much more interesting and fun than just using a capital ship tractor beam. Having the player chase down ships and disable them, then having to guard transports carrying boarding parties, it makes for some really fun missions. A definite alternative to the default "kill everyone" style objectives.
You can make some canonical arguments that ion cannons were the main method of capturing ships:
The first is that ships such as the Y-Wing and B-Wing definitely carried ion cannons, and from the Battle of Hoth it can be seen that the primary effect of an ion cannon is to disable a ships subsystems. So it seems likely that the reason Y-Wings and B-Wings carried ion cannons was to disable enemy ships. Additionally it suggests that ion cannons are the best option for disabling a ship, because if you could do it easily by targeting subsystems with laser cannons then the Y-Wing and B-Wing wouldn't need to equip ion cannons.
Secondly although capturing ships with tractor beams is mentioned in canon perhaps this only possible in quite limited circumstances. The tractor beam might have quite a limited range, or maybe it can only reliably stop targets if the target is in a certain position.
Thirdly the fact that ion cannons don't appear to be used extensively in the Battle of Yavin or the Battle of Hoth could easily be explained by the fact that capturing things in those battles wouldn't have been a high priority. They were full out assaults aimed at total destruction of the enemy, laser canons would have been a better choice for this kind of engagement.
So all in all I like ion cannons. They make some really interesting missions possible

The canon material seems to be ambiguous on the subject, so personally I think it makes sense to chose an interpretation that makes a good game
