We don't have an indoor facility in our state. However, I have officiated every one of the Twilight meets that my old high school has ever held, a meet that has grown to over 3,000 athletes. I'm now the meet referee. So a few thoughts:
1. every facility has only so much space and time. There truly is a limit to how many kids can participate. Finding where that limit is is probably not high on the agenda of meet management. No meet director wants to say no to entries. They want to give kids the chance to compete. Our facilities allow us to do more than most schools. We have two pole vault pits, two shot rings and three horizontal jump runways. So, for example, the top seeded vaulters are on one pit and those with lesser marks are on the other.
2. it's all about the details. There are a lot of little things that can increase or decrease the efficiency of meets. There is, therefore, no single, magic fix. Do (field) events start on time? I mean, exactly on time? "Just one more run through?" "Sorry, no. Smith is up, Jones on deck, Brown in the hole." Do you have a clerk of the course on the track, getting the next race's athletes lined up while this race is getting started? Or do you expect the starters to do that? Do you have a marshal getting runners off the running surface as they finish? And do they get medical out there immediately if a finisher goes down? What's the opening height for vertical jumps? E.g. high school girls' high jump. If you are starting at 3'6", it's going to be a very long day. Yeah, I know everybody won't get a mark but that's what practice is for, learning how to get an opening height. I did one high school meet where the coach sent a girl over to do high jump. She was approximately 4'3" tall! The opening height was neck level for her. What are you doing to that kid, coach? Not surprisingly, she ran at the pad three times, knocked down the bar and she was done for the day. IMHE, minimum marks to be measured in horizontal jumps don't save that much time. Having good rakers, and two or three of them, can make all of the difference in the world.
3. good officials get things done. Poor officials can't figure out what happens next, so they have to ask somebody else. When they can find them. Particularly teenage athletes need leadership. "This is what we're doing." Loud and clear. No "who did you say is up?" Silly, but the 20 seconds you lose every time they don't know who is jumping or throwing next adds up pretty quickly.
4. what events are you running? For example, maybe you deliberately limit the 200 M entries to only get the better athletes, but you do run a whole bunch of 4 x 200 M relays. Less time to do a relay than run the same number of runners over four heats of 200 M.
5. how big are your heats for races not run in lanes the whole way? I've seen 30 and 35 high school runners in a single heat of the 3000. Yeah, somebody gets to count laps but, especially with high schoolers, they get strung out pretty fast. Amazing, though, to see the pack, maybe six abreast, come around that first turn!