I won't lie, as convenient as it is for players to rack up dozens of legendaries something about being able to do so does sort of cheapen their legendary status. That said, the EX system as is wasn't the answer to that. To your points specifically;
-The February round in question was an accident, as people received passes to gyms they had previously spun maybe once. That round should not be considered in the EX assessment.
-EX raids as is are too limited because standard raid constraints are forced upon them. Having raided at a particular gym isn't much of an issue as connectivity with your local raid scene should narrow down what is and isn't an EX possibility. The EX raids being 45 minutes is the biggest hang-up; why not allow the raid to run all day so that groups can decide a week in advance if raiding it in the morning/afternoon/evening would be best?
-I mean, I'd be much more inclined to do a one star raid at a gym I knew handed out EX passes than one that didn't. This falls back to being in tune with your local raid scene.
I'm not saying the system is perfect or that rural players aren't dicked over by it. I'm just saying that for a lot of arguments there's a weird method to their madness, and while it can be improved upon greatly it does make some modicum of sense.