I flew from BER airport two weeks ago. I had low expectations after reading lots of negative reports but I was pleasantly surprised in the end. It's not by any means the world's best airport and for a new airport it's a bit disappointing but there wasn't anything massively wrong with it, certainly it isn't any worse than any of the UK airports, and I'd be happy to fly from BER again.
BER Airport is well connected. The S-Bahn runs frequently from the centre of Berlin to the airport and there's also the Flughafen Express (FEX) from Berlin Hbf, Gesundbrunnen and Ostkreuz stations fast to the airport. Unlike most Airport Expresses there isn't any premium to use the FEX, local transport tickets are valid as is the Deutschlandticket.
My flight was from Terminal 1 however it's worth noting that both terminals are connected airside, so you can use the facilities of both terminals regardless which one you're departing from.
The regularly reported security chaos can be avoided by using the fairly new Runway Security in Terminal 1. Basically you book a time slot for security, turn up at the time you've chosen (you'll be accepted 10 minutes either side) and go straight through a dedicated security area without queuing. It's free of charge too.
Do however remember to buy anything you may need for the flight before passing through passport control if on a non-schengen flight, as the retail facilities after passport control are very limited.
I didn't find seating to be an issue at the gate, there was sufficient seating for 180 passengers on an A320.
I can't comment on arrivals at Berlin as I flew in to Frankfurt (not a fun arrivals experience but still better than Heathrow).
You may wish to be aware with Prague Airport that there's no rail link so the only public transport access to the Airport is a bus.