I have a SD who is 6 and lives 1200 miles away. DH and BM got divorced when SD was 2, so I have some experience and opinions about some of what you're talking about. These are just my opinions formed by what DH has gone through and what I've researched.
I think the most important thing to remember is that your daughter is going to grow up not knowing what it's like to have intact parents, so what you perceive as stressful to you won't be for her because it's all she's ever known. Therefore, you should not think of your home as her only home. You seem to be thinking as your house as her place of foundation and stability, but the courts may not see it that way. Unless there are some other underlying things going on with the child's father, the court is going to look at his home with the same importance as your home.
DH and BM's divorce decree never prevented any overnight visits and remember, SD was 2 at the time of the divorce. When BM denied an overnight visit when SD was 3, I did a TON of research into the subject and actually found that you shouldn't wait to start overnight visits. It's not unusual for very young babies to have overnights with a dad, especially when the child isn't nursing. If you truly want your daughter to have a normal relationship with her father, then you need to allow him the time to build that relationship and I'm not sure some of the controls you are wanting to introduce will help him build a relationship with his daughter.
Why would you want supervised visitation? I'm not sure the child's development will be helped or hindered by seeing the two of you interact. You will do more good by always talking positively about the father in front of your daughter than you would trying to force a good in-person interaction. Why only 3 hours? If he lives 900 miles away, he deserves more than 3 hours of visitation at a time. He should be able to do the every day things you do. Feed her, bathe her, change a poopy diaper, put her down for a nap. A 3 hour visit feels like an uncle visiting or something, not a father.
Another thing you should consider is the place of the visitation. You're wanting him to stay close and not do visitation at his house. There's nothing more unnatural than doing a visitation at a hotel room. BM had a problem "letting go" of SD and allowing her the opportunity to visit with her father in HIS house. She actually hid her when it was time for her first plane trip to our home. So that's now 2 contempt of court charges against her. BM didn't want SD to leave the city, she wanted the visits to happen in her town which meant getting a hotel room. Try putting yourself outside your situation and imagine only being able to see your dad at a hotel room. You don't know what his house looks like, you don't get to play with his dog, you don't get to see your own room, etc. Again, this goes to a child's ability to establish a solid relationship with a parent. The good thing is that kids are young and very flexible, so SD barely remembers the visits in hotel rooms and now has a ball at our house.
The agreed location part is also a little suspect. It's my understanding that the law allows your EX to be able to do anything he wants with his daughter during his visitation time (as long as it's not illegal, abusive, or neglectful). This may not be the case with you guys, but with a lot of parents, anytime something says "agreed" it's a license for one parent to sabotage something by not agreeing just for the reason of not agreeing. You don't have to answer to him on what you do with your daughter, so why should he?
Try not to make the times so restrictive. One thing I've read is that people's lives change and you want to have reasonable boundaries but also leave a lot of flexibility because who knows where each of you will be a year from now, 2 years from now, etc. Maybe a Friday overnight would work better for you/him. Don't box yourself into such a restrictive schedule.
Until your daughter starts kindergarten, you should consider the possibility of visits during the week. That goes back to being flexible.
Some of your other questions...
I would start overnights earlier rather than later.
Don't put in hard rules for increasing visitation. Try to remain flexible.
Your child should be able to travel (by car) with her father anywhere and at any time, as long as he has the proper car seat.
DH's decree says no traveling alone on planes until 12, but the decree was written right after 9/11 and I have found that 12 is VERY old to start traveling alone. Most people I know let their children fly alone much earlier (but ONLY on non-stop flights!).
The only other non-standard thing in DH's decree was about summer visitation. The standard is 42 days. DH's decree says that until the summer after kindergarten, the summer visitation can not be longer than 14 consecutive days. So DH could still get his 42 days, but he would have to break it up into chunks so his daughter wouldn't be away from home longer than 14 consecutive days. SD was 6 the first summer she could spend the entire 42 days with us.
I hope this information helps. I have a son who is getting ready to turn 1 year and I remember quite vividly how protective I was of him when he was first born. I didn't want any one breathing on him much less anything else. I know it's hard to think about visitation with your EX. Your body is a hormonal mess. I think that if your ex wants to come spend the day with her, then you should be open to that. The worst thing you can do is try to tell him how to be a father. Daddies will never do it like mommies and that's OK, that's what makes daddies (and mommies) so special. I know your family is mad, but do what's best for your daughter and let him in her life without so many rules and restrictions. The more you try to control him and his actions, the more you will drive him away.