For many aircraft types there are many engine options and they are all offered at once the type is placed on market. However, many engine options are only certified in a later stage. For example, the Airbus A320-200 was introduced with the CFM56-5A1 certified in 1988 and IAE V2500-A1 certified in 1989. Later the CFM56-5A3 was certified in 1990, IAE V2527-A5 in 1993, CFM56-5B4 in 1995, IAE V2527E-A5 in 1995 and lastly CFM56-5B6 in 2006.
What I'm suggesting is that airlines can only order aircraft with a particular engine option maybe a year or two before it is certified and the aircraft can only be delivered after the certification date. So this means that airlines can only make do with the present engine options offered at the time and would have to wait for other new options if they wanted them instead. This wouldn't make the system complicated, it will be like introducing a new aircraft type. News of the engine option being offered would be announced and that option would appear on the choosing engine type page. I'm sure this would make the game a little more interesting!