I think it is based on the fact that they both have some sort of darkness around them in their songs or dressing. I don't agree that the two are similar in any way because I think Lady Gaga reminds me of Madonna as opposed to Marilyn. It could be also possible that he influenced her work like the mechanical era and she has drawn a similar style from him which would make them seem alike in some way.
I agree with both baby.ruth and guy85. I think the general similarity is: They are wierd and have followers. Baby.Ruth makes an excellent point with Lady Gaga. I feel Lady Gaga is the Madonna of this generation. Both make a clear statement saying it's o.k. to be who you would like to be. As long as you don't hurt yourself or anybody else, be who you would like! Take Care and have a great day!