There is actually a lot of structural similarity:
Both started by a true crackpot with delusional ideas. Both men named themselves a special prophet to the world.
Both saw this original guru supplanted by a come-from-nowhere new leader who wrested power away from the chosen successors by deceipt.
Medical Contraversy - Witnesses: the vaccine hatred, the later blood ban. CSI - hatred of psychology, anti-depressent drugs, proponent of various near-quackery "self cures". Both promoted pseudo-scientific "healing or analysis" electrical machines at some point or another.
Control Freaking - Both groups cannot be called anything other than "extreme high-control organizations".
Centralization of Power - Both the early JWs and more recently CSI destroyed their older "independent" congregations and brought it under central control of the governing corporate authority. Brutally and without warning, as a matter of fact.
Theological Weirdness - dealers choice here. I could not really pick: a) Xenu the evil alien who put all evil souls in the universe into volcanoes on earth and blew them up with hydrogen bombs. b) War-god YHWH who is coming very soon to kill almost all the 6.6 billion people living on earth because they are not converted to JWism.
Hatred of Government - again, take your choice. Brought on by numerous lawsuits, tax evasion issues, personal liberty issues, etc - but in both cases, things they did themselves caused the "persecutions".
Love of the Occult - while both deny this, there are numerous Occult ties to each, and each secretly believe in decidedly strange occultic phenomenons even today.
Money Grubbing from Members - Scientology wants you to make as much as possible, and then give most of it to them. Witnesses want you to make as little as possible, spending most of your time selling their magazines and recruiting, and then give a good part of what little you do have to the "worldwide ministry".
Six of one, Seven of the other. Both are really too weird for words.