These 3 leaks you refer to don't exist in our dojo or the ones of other styles that I've been to (not saying that we may not be lacking/leaking in other areas). So I'd tend to agree with the folks that believe this is more of a dojo's internal approach to training rather than something that is an epidemic in all Aikido.
On my first day of training in Aikido I was taught that Aikido teaches you to attack properly (i.e. correct form to be most effective in attack), thereby allowing one to deeply understand both sides of the equation of Uke and Nage. E.g. when dealing with hook punches, haymakers are totally outlawed, it just makes things too easy and unrealistic in the event one happens to be at the wrong end of a serious hook punch.
For things like competition and self defence training anything but a correct and committed attack ends up in a delusional Tori (as to his true abilities) or an Uke who takes a lackluster approach to training, which can be just plain dangerous.
As far as Atemi goes, Atemi Waza (application of Atemi as a throw/kuzushi) tends to aid the practitioner in understanding both control in targeting and entry, as well as how to apply the full percussive strike if necessary. Practicing against heated resistance, one has little choice, or such techs like Irimi Nage (Aigamae Ate) just don't work in those conditions.
Alternatively Uke needs to understand how to respond to quick, powerfully delivered atemi waza, else getting knocked out can be a reality in intense training. Again, awareness and sharpness adding to one's own safety.
Maybe a way to address these leaks can be to gradually increase the degree of intensity in the dojo as far as honesty is concerned with attacks. Things like not allowing weak attacks to escape the scrutiny of sensei and seniors, addressing these things immediately and showing the benefits of both ways of practice (i.e. weak and strong attacks), then slowly developing the practice to a point where strong attacks prevail and the resultant training environment is more martially sound. I've found that weak attacking consistently over time can severely degrade the integrity of training and even the martial spirit of a dojo as practitioners enter an automated type of training that is martially meaningless.
Of course though, it depends on the training objective, I've been to dojos where sensei say pointedly that they do not belive Aikido is a martial art. All are privy to their opinions.