Well we ended up going with Gekko Trails Explorer, so thought I'd better post our thoughts on them in response to my own question.
Overall, we had a really good service from these guys - admittedly, the trip is long (advertised as 15 hours - our experience was 16.5 hours due to traffic jams on San Salvador and Guatemala City), but if we want to get from Leon to Antigua and miss out the bits in between, then I'd highly recommend this shuttle. From what we could establish from others, Tica bus (and similar) would have required an overnight in San Salvador and would have lengthened the trip to around 30 hours (including the stopover). While Gekko were US$79 and therefore more expensive than Tica, we saved on the night's accommodation.
Positives:
- they picked up on time and from our accommodation (a real positive when it's a 3am start in a dark, deserted town)
- comfortable, executive class, shuttle buses
- all luggage kept inside bus
- movies/pop videos played for journey (although thankfully not for the early morning leg)
- smooth border crossings - we only had to leave the bus to enter Guatemala - all other crossings were handled by the driver or a border official coming to the bus
- friendly drivers, who speak english
- regular comfort breaks and stops for breakfast and lunch
- air conditioning - a bit too cold at 3am, but certainly not at Tica bus levels of coldness
Negatives:
- the 3am start (but necessary to get you to Antigua by early evening)
- if one person has a problem with immigration at the border, then the whole bus waits (same with Tica bus)
- no on-board toilet (but enough breaks during the trip)
- they drop off only in one (central) place in Antigua - you're then on your own (while Antigua streets are laid out in a straightforward manner, they don't have street signs at every intersection)
Overall, we're really glad we took this shuttle - it was perfect for the journey we wished to make, and the service was great. Recommended.