As to taking ukemi, I also remember the first time ‘we' trained a police officer to take a high fall from kote gaeshi and he got up and said, "My wrist doesn't hurt!" Duh, that's why we learn to fall properly.
And that reminds me when I saw a Gracie competitor taking 6 aspirins before his match thereby eliminating pain tolerance but if cut in a real fight would have bled like a stuck pig. It also reminds me of the competitive MMA fighter who squealed (again like a pig) when a finger lock was applied.
There is a reason that wrist / finger / and pressure point fighting (yonkajo) doesn't make it into the ring. Too much damage and yelling.
Back to Aiki. Difficult sometimes to get right, worth it when it does. Takeda Sokaku worked on two principles -- Aiki and pain. To say otherwise is to discount history.
I think you're spot on here. I attended an aikido seminar last weekend. The teacher is very good, good technical stuff, but it brought home to me just how tough on the body aikido has become. The large movements and getting off line/relying on uke's momentum puts huge strain on joints (on both uke and tori), and it doesn't make it more "martial".
I noticed there's a big interview with Christian Tissier on the aikido journal site about the future of aikido. I think a big challenge with aikido is its excessive physicality without the initial body conditioning/kihon. There are whole generations ending up with wrecked bodies in their 40s and 50s because they did the big flashy moves popularised by people like tissier, and/or full on arm bars/locks pain compliance etc. This kata based practice that some scoff at here is actually the method for creating a kind of body that can actually practice for a lifetime. If people want to take that then and use it for physical damage, that's a different coversation, but personally, I think the most important thing for any traditional system to teach is a correct and healthy body method that can then be applied to forms. This has been majorly neglected especially outside japan, in favour of muscle/reflex driven damage IMO.