I fly a lot for work but it's a small company without any corporate travel department or rules. We book what we want but all the travelers are also part owners so being extravagant with travel expenses hurts your wallet. So I don't have any suggestions for dealing with corporate travel policies.
I agree with the idea of trying to stick with an airline or two. Getting enough miles/segments to get to a premium membership level is huge. Short lines, frequent upgrades, free baggage and general good treatment by agents throughout the system. Nothing is universal but when your boarding pass says "Premier" or "A+ Elite" or "Platinum Medallion", the process of getting in and out of airports can be a lot less of a hassle.
Join a couple of rental car programs. I rent almost exclusively from Hertz because they NEVER hassle me about anything. They seem to accept that small dings and parking lot scratches happen to cars in daily use and ignore them. I've had other, more discount oriented companies, try to collect from me for silly little incidental damage that may or may not have occurred while the car was in my possession. I never do a walk around inspection of a car at Hertz. I ALWAYS do it at Budget or Dollar or Alamo, all of whom have tried to ding me for normal wear and tear items. I'm not talking about crumpled body panels or broken lights. I mean nicks in the windshield from a rock thrown up on the highway, scratches on a bumper from some middle of the night douche brushing my car in a hotel parking lot etc. Never once has Hertz bothered me about that kind of thing. And, with rare exceptions, my car is waiting when I land.
Learn to use time in airports productively and then you can not worry about trying to schedule your flights to perfection. I frequently show up at an airport 3 or 4 hours before my flight, check any bags I'm not going to carry on, get something to drink and sit down and get some work done while I wait to fly. (you have to learn to manage battery life as electrical outlets can be hard to find in most airports - try looking around unused gates)
Learn TSA and don't buck it. By the time I get to the point where they check your boarding pass and ID, the only thing left in my pockets is my boarding pass and ID. My shoes are untied, my phone is tucked in my carry on, I'm ready to take out the laptop,slip off my shoes, take off the belt (only if they're using body scanners, my belts will go through the regular metal detectors no problem) and walk through. You won't find me standing at the table fishing keys, coins and whatnot out of my pockets (Why do people travel out of town with their personal keyring in their pocket? Mine goes in a particular spot in my carry on bag as soon as I park my car at my home airport.) You can't get around the security circus. The best thing you can do is become expert at flowing through it. Premium FF status will get you in a short line in many airports but not all. In some locations, those lines actually end up longer and slower than the regular line - take a look before committing.
My hotel chain of choice is Choice. They are everywhere and as long as you stick to the top two or three chains in the umbrella, most are quite decent. If I'm staying in one spot for more than one night, I look for rooms with a refrigerator and microwave for keeping cold drinks at hand in the room and re-heating leftover carry out dinner stuff for breakfast. I carry coffee with me a lot. I get up early, but make my own coffee in the room and get morning work done (email, miscellaneous tasks that require sitting at a desk with my laptop on and my head straight) before ever leaving the room. I rarely eat the free breakfasts at hotels simply because I'd rather have something in the room head straight to my car when I walk out. I hate eating by myself in a restaurant so I usually pick up carry out from one of the casual dining chains and eat in the room. There, I can watch TV or do a little work while eating rather than sit and stare at people I don't know at the next table.
Second choice is IC which is Holiday Inn or HI Express and HHonors is third. I used to be a Hampton Inn regular but Choice's rewards program won me over and a lot of Hamptons started to get a little worn out. On the rare occasions when my wife can talk me into traveling for pleasure instead of work, I can almost always book free hotel stays anywhere we go through the Choice system.
All of this hotel stuff can depend on what kind of traveling you do - major cities are different from small towns, which is where I do most of my stays.
Overall, I try to minimize the disruption that travel represents to my life. I have to travel for my job. But I can feel at home in a hotel and I can ease my passage through the airport/rental car mill and I can avoid being rushed and harried.
If you have to make flight connections, be very conservative with the connections times, especially during the spring and summer when weather disruptions are the rule rather than the exception. A few thunderstorms around just a couple of major hubs can disrupt flight schedules all over the country. If you book 30-45 minute connections at big hubs like ORD, ATL, SLC, BWI or PHL, you are just asking for missed connections during the summer or at least setting yourself up for sprints down the concourse. Cooling your heals in row 24 while watching the minutes tick by can be seriously stressful if you have a tight connection. The FA's will ask people to wait if they don't have a connection but in most cases, in my experience, that request is largely ignored. Everybody has someplace to be and wants to get off the plane. I'll wait, but I don't see a lot of people doing it.
Traveling is tiring and time consuming but doesn't have to be stressful. For me, making it easy makes all the difference. I actually look forward to getting out of my rental car at the airport a lot of times because I know that from that point on, I'm basically going to relax until getting to my next destination. That doesn't mean I'm going to waste the time but I'm not going to hurry or worry or stress over schedule or procedures etc. I'll flow through it and get out at the other end somewhat rested and ready for the next destination or, sometimes, home.