My first GenCon was overcrowded like you describe. Since then I've made it a point to only go with 4 to a room maximum. It was definitely more enjoyable when I was only sharing a bed with one other person instead of sharing a bed room with 6-8 people.
In the years that I've gone, I've tried a lot of different 'solo' scenarios...
* Fly or drive in solo, but arrange room and roommates online via whichever forum you choose. Generally, I've handled this via Hordelings.com a forum for fans of the D&D Miniatures game... because I was a really big fan of that game and most everyone I've met through it is pretty cool and I wouldn't mind sharing a room with them (apologies for the run-on sentence). I would have probably done it through ENWorld if I was more into organized play like LFR.
*Fly or drive in solo, stay at an inexpensive place away from downtown. This required a bit more effort. This works a little bit better if you drive than fly (I've tried both). There is a nice youth hostel on the north side of Indy that is very inexpensive. There are also a lot of motels on the outskirts that are relatively cheap. If you're into camping, there are also some campgrounds in the metro area. The main downside to this is that you have to drive back after a LONG day of gaming... and there will definitely be times when you want to hang out late into the evening. Having a room nearby makes life so much easier.
*Somewhat related to the last option... stay with a local. If you don't happen to know anyone in Indy, then you may want to join something like couchsurfing.org. I've been on both sides of this as a host and a hostee (is that even a word?). I've had positive experiences on both sides of the equation... and one year when I was low on cash, I used this successfully to stay with a local for GenCon. On another year, I used it to just meet a group of locals for drinks on the night before GenCon started since I already had a hotel room and I had that night free.
If, however, you have the money to stay downtown... that is by far the best option. You don't necessarily need to go solo. Just find one or two other people to stay with to defray the costs if you like. If you haven't found a room yet, check the GenCon forums. There are always people that back out and will transfer a reservation to you. I've done that several times and it works great.