Some people do not like the first method "thumb leading rest of your hand around the wrist of attacker" because it's easier to lose the grip on uke, thus allowing uke to escape... what do you think?
Depends if you are talking about ‘kihon' presented at the test or ‘application' where attacker has more freedom to react. In the first case you need to improve as much as possible both ways, it will give you a bit more freedom to adjust when practice different aikido styles.
In the second case -- it is completely other world. Usually one hand that controls attacker elbow during transition is not enough to really control countering attacker. I like to put attacker forearm between my hip and thigh to add additional leverage control with my weight before attempt to change from ikkyo to nikkyo. Then the way how you change has much less importance.