I don't think uniformity will sell toys to children, not unless it's cheap generic grunts or baddies. I suppose that there is room for differentiation in their webgear, headgear, faces and weapons (though that then moves away from the whole uniformity thing
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On the other hand, there are a fair few environments and roles available, so there should be room to produce figures that are different but still realistically and uniformly uniformed for their environment/role.
I'd certainly like to see some more generic camouflaged figures (Woodland or DPM and Tiger Stripe, mainly as those are what I liked as a child - I think the newer MTP and Crye are too complicated and small for the scale, or perhaps they just work too well and mean you don't see the figure's shape as well - I think less is more with the camo, as long as you get an impression of the pattern without needing too much detail and the factories doing the paint apps will probably agree)
I'm indifferent about whether the characters should be kept, I love the Marvel comics, but I realise a reboot might be in order, but equally throwing away all that potentially useful backstory isn't necessarily a good idea.
Ninjas good, but not many, adds to the mythos.
Space good, but fairly realistic - there's a whole environment which could be exploited there (and with the advent of commercial space flight and the tests currently underway for things like Mars landers it would surely make sense).
I think Adventure Team should definitely be resurrected and refreshed, probably with a separate storyline and characters but with cross-overs (and using the same moulds for figures and vehicles) - there is just so much mileage in the idea of adventure and exploration with the natural world as the unknown/danger rather than a group of baddies. As a child, while I spent a lot of time with my Joes fighting (Cobra, VietCong, Argentines, etc.), the vast majority was spent in adventuring - climbing, parachuting, test pilots, space, etc.
With the above Adventure Team idea in mind, there are lots of interesting things going on that would stimulate children's minds (and not be military and be educational, which might appeal to parents), e.g. RedBull Stratospheric Parachute jump; the aforementioned commercial space flight, Mars/Moon mission planning, and things like SpaceShipOne's test flight; the slightly disappointing race to the bottom of the Mariana's Trench (only saw one competitor, and the DeepFlight which looked to be very cool never even got rolled out afaik). Then there's just the standard stuff exploring mountains, deserts and jungles, caving and cave diving (I just watched Sanctum).
Sorry for the essay!