To my own understanding, you should not move into resistance. Regardless of using internal or external force, your movement should feel free even when UKe is resisting.
But, this is much easier said than done, especially once Uke knows your technique, and is on a level comparable to your own.
As a general rule, once you face resistance is starting to build in a particular direction, your technique should shift a little to either go around it, or tunnel through it or roll over it, depending on the exact situation , while generating power that is harder to follow and resist. Or, if the resistance is too strong, you may wish to use it to get into another technique.
It is pointless to practice a technique directly against resistance, since if you can do that, you could simply grab the guy and throw him with force - and the technique is not needed.
Training with the existence of resistance, is not the same as working directly against resistance. As mentioned above, one should be able to do his Aikido even when Uke is resisting, it would not be the Kata Senei showed, but it would be Aikido.
And Ukemi is not just simple recpetion, it is a much more subtle issue, which is at least as important to "martial effectiveness" as doing the techniques.
Students need to have permission to allow their technique to be what it "wants to be" rather than training themselves to force their partners into some predetermined form demonstrated by the Sensei. Otherwise you are simply training them to force their techniques and killing their sensitivity. Very bad martial arts.
If you consistently find you can't get the technique shown on a given partner, ask the teacher for help. See what he does when he or she throws your partner. I usually say "show me" when someone says they are having trouble. Often I see that the uke is giving an attack that doesn't lend itself to what I had shown. So, I explain this to the student and show the uke how to deliver the kind of attack that makes what I was teaching make sense. I also let the nage know that he wasn't stupid for not being able to do that particular technique.
This is so important... so much of our training is about trying to pound a round peg into a square hole. It's crazy and doesn't ever result in a decent level of skill. Training should be about, first developing the sensitivity to tell whether the hole is round or square and responding appropriately and then later, understanding how to get the partner to create the shape you want him to be in, preferably without him being aware that you did so.
Anything else will simply result in either manhandling the partner into the shape you want, or having uke collude so that your stuff works.