Maintenance price is based on age. Maintenance raises aircraft condition and flight hours/cycles lowers it. Price is a function of age and condition.
So they are all connected already, but maintenance is done based on age instead of flight hours/cycles. I assume this is, in part, because it uses less resources using a simple cron job to check every aircraft every 4 game weeks instead of checking flight hours/cycle values every game day which would be a significant load on the server.
In regards to stored aircraft, the solution IMO is to simply freeze the maintenance clock on those aircraft, so if you put in in storage with 4 years until D-check and take it out in 2 years, you'd still have 4 years until D-check (not 2). However, I think the last thing sami wants to do is promote the idea of putting planes in storage as he'd rather encourage players to lease them out and create liquidity in the used market.