Good thread - an interesting read!
Re 1, i'd suggest there are thousands of variables that would keep airport planners up at night, but some that immediately spring to mind;
- ability to get to/from the runway quickly - that would include minimising dead time on the runway before turning off at an intersection and also the ability to get to it quickly/efficiently. For the latter, think of a junction on a major road - if that junction cant cope with the amount of traffic coming at it, it wont be able to efficient shove traffic onto the motorway, even though the motorway might have stacks of capacity remaining. Having rapid exit taxiways, for example, in just the right spots for the major aircraft types will speed things up hugely.
- aircraft handling - or in effect everything from getting off the runway to getting back on the runway, including all of the aircraft servicing. I don't know the short/long haul split, and how that compares to, say, Stansted, but any myriad of reasons from employment contracts to facilities to x or y or z could impact the ability to turn aircraft around quickly
- number of stands - are there enough, incl. of the right type?
- weather - Gatwick operates more or less flat out every day throughout the year with no real weather issues. Does Prague suffer (at all) when its snowy? I'm not saying it falls over completely, but if everything takes a couple of minutes longer that amounts to a substantial reduction in capacity
- seasonality - UK airports are fairly busy all year round, particularly in London. Is Prague the same?
- Planning restrictions - 21m might be on the basis of noise etc. agreed many years ago. It could be argued (Heathrow do) that having another runway allows that noise impact to be spread out so could be a reason to explore it?
- Resilience - i think this is common in the US. FLL for example managed to get a new runway because delays on its existing runway were causing (evidenced) knock on delays across the entire USA, despite only having half the number of passengers of, say, Gatwick. (as an aside, wouldn't it be good if the EU managed airspace/airports across Europe and could use this argument to expand airports this side of the pond, so the 'knock on delays' argument might actually have some legs - maybe Heathrow might happen in a reasonable timescale then!)
There are bound to be more. All of which is to say that it wont be easy to compare two different airports.
As a further thought, talking about passengers may be a bit of a misnomer. Perhaps you could consider ATMs. Do they have dedicated cargo flights, for example? or perhaps they are full to busting in terms of number of aircraft they can land/service a day, but they are all tiddlers (i.e. the passengers per aircraft figure is very low). Having a second runway could allow a diversification of destinations, e.g. allowing more long haul into the mix on bigger aircraft.
To go off on a bit of tangent, a similar debate can be had re active traffic management, e.g. controlling the flow of traffic to maximise capacity/throughput - the principle used on Smart Motorways, for example. This video is useful;
The reason i raise that is this - if you leave a road as it is, with ever increasing traffic, safety begins to be an issue, normally commencing with nose-to-tail collisions. Increasing capacity, whether through technology to better manage the flow or through building extra infrastructure, allows that traffic to flow better, and safety improves (to a point).