Aside from what Ensapa pointed out about the Maitreya project etc, I think the singularly biggest telling sign that something is wrong is that Lama Yeshe's incarnation, Lama Osel, has not stepped up into Lama Yeshe's shoes to be the successor of the organisation he founded - FPMT.
That Lama Osel is Lama Yeshe's incarnation is indisputable. Lama Osel's interest in Dharma and his closeness to Lama Zopa throughout the years is proof that he is who he is. However, i believe that as long as there is the ban on Dorje Shugden at FPMT, Lama Osel will not step in officially. This is regardless of whether Lama Zopa is secretly practising, because if the rule of the organisation is anti-Dorje Shugden, which is against the heart practice of its founder, Lama Yeshe, then the karma of the organisation will remain thus so.
Lama Zopa is not getting any younger and i hope that FPMT will quickly act to address this issue. The first step would be to remove the ridiculous requirement that Dorje Shugden practitioners are not allowed to join FPMT activities. The organisation need not immediately start the practice out of respect to HH the Dalai Lama, as Lama Zopa has stated, but the very least FPMT can do is that they quietly remove restrictions on Dorje Shugden practitioners, don't you think?