Well, it takes some time for a new player to get the hang of how Airline Empires work. I'm still not even a full month into playing the game, and I already got myself familiarized on most of the game. However, I believe I can answer some of your questions.
1. Well, keep in mind that Airline Empires is a more realistic airline tycoon game, and so far is the most realistic one I've played to date, so when you're managing your routes or setting up a brand new one, it doesn't tell you that, oh, this is First Class, Business, and so on. Instead, the game uses a system that some airlines would in real life. F being First Class, C being Business Class, and Y being Economy. And as for how ticket prices work, I've never seen altering the business class tickets having an affect on economy. Basically, business class needs to cost more than economy class. Otherwise passengers want to pay the cheaper price for more luxury, compared to the more expensive price for less luxury. You basically got to make sure the ticket prices are fair for a certain class people. You can tell if you have a good ticket price by changing them, then saving them to see what the new price's impact is like on the route in terms of load factor for the route's weekly flights, and the overall daily profit from the route. I try to hit that sweet spot of having the load factor barely at 100%, or at exactly 100%, but yet trying to get the most amount of money off of that specific route from one certain class of passengers.
2. Well, let me go on ahead and explain how a route's frequency works. It basically means the number of weekly flights to that destination, and how convenient it is to passengers if they want to travel on that specific route. For myself, If I'm operating on a route with no competition what-so-ever, such as Pittsburgh International Airport to Syracuse Hancock, I try to set up a good amount of weekly flights that would fill up the market in terms of passenger demand. Of course, I prefer putting in not too little flights, which means less profit for your airline; And not too many flights that have some leaving not full. Once again, like the ticket prices, there's a sweet spot too for the number of weekly flights.
As for a route's reputation, that all depends on what you have available in terms of both In-Flight Entertainment, and In-Flight Services. In-Flight Entertainment can vary on how you want to entertain your passengers on board, to help a long flight feel a lot shorter, which could be from the cabin movie projectors you'd find at the start of 1961 in the game, to some IFE systems you see today like Audio On-Demand, Video On-Demand, flight tracker, and Live TV, just to name a few. And then there's the In-Flight Services, In-Flight Services is key for helping your passengers feel more comfortable during their flight, such as in terms of catering (food) and some accessories that you would find on the ground, and that a lot of airlines in real life offers. These accessories can be pillows and blankets, newspapers, and comfort kits, just to name a few.
If you can get a good balance of both In-Flight Entertainment installed on your aircraft in your fleet, and a good amount of In-Flight Services for your passengers, then it'll boost up your routes reputation a lot, which would mean more passengers flying on your airline!
3. Well, like what I said earlier, it's all done by weekly flights when you set up new flights. Even though the game shows its income as daily profit, flights are usually managed by how many you do on a specific flight per week. A good example would be the real life airline, JetBlue Airways. For them, they do flights from Orlando International to Syracuse Hancock 7 to 10 times a week, because that route doesn't have as much demand as Orlando International to New York's JFK, which that one has 35+ weekly flights. Like what I said earlier, there's a sweet spot for your weekly flights on your routes to make the most out of them. So, there's no need to do these huge mathematical ratios to make things even for all of your aircraft in your fleet. Just use the hours that your aircraft has available on which routes you want to fly them on, and you're all good! As long as you're getting the most use out of your aircraft, and it's still making a good profit for your airline, then you're doing the right thing with your fleet and route.
4. As for on-time performance, I'm not entirely sure on how that works.
5 & 6. Good question! I really never picked that up yet. Maybe someone from the admin or development team would pick it up and fix it in the next time A.E. needs maintenance.
Well this may seem like a lot of information for you, Benem, but I hope that I did help you out in some way on getting a better understanding of Airline Empires. I wish you luck on keeping your airline up in the air!