I think it comes down to what you want to achieve. A spaced-omni technique doesn't give any front/back separation. If you're just recording a general ambience effect that obviously won't matter and may even be a bonus. But if you're after a sound in a specific location, some directivity to focus on the wanted source and reduce any unwanted ambient sounds may be more useful.
Using shotgun mics for stereo can be done, but it's very easy to have a big hole in the centre if you're not very careful, and off-axis sound sources can be very phasey-sounding, especially if they're moving in relation to the mic array.
Personally, when I'm out and about recording natural sounds I tend to use an MS pair (Sennheiser MKH 30/40 or 30/50 usually, sometimes a 30/20 combo) in a Rycote Cyclone windshield, supplemented with a pair of spaced DPA 4060 Cores (personal mics) which are mounted on FM radio aerials to allow me to easily adjust their positioning. All recorded onto a Nagra VI.
Or if I need to be more compact, I'll use one or other of those rigs feeding into a Sound Devices two-channel preamp with MS decoding and monitoring, and record its (unbalanced) output onto an Olympus LS11.