I haven't fully grokked this yet, but one trick I've used in the past to get around limits is AWS Organizations, creating a sub-account per property. A bit more setup but can keep things cleaner administratively.
At least for the tests I've done on a small startup recently, they've also implemented some automatic quota increases for EC2. I ran commands that would have (or did) eclipsed my quota, and got an email that my quotas were bumped a few minutes later.