Brit Ahuvim and other ideas...

If you're looking for something that isn't the traditional kiddushin, but rather an alternative Jewish ceremony, Rachel Adler suggests a brilliant solution that she calls Brit Ahuvim (Lover's Covenant). You can take a look at chapter 5 in her book Engendering Judaism to learn more about it. Rachel Adler is very knowledgeable in Jewish tradition, and is very committed to it, but she brings to it an amazing creativity and openness. i'd say it's worth a read even if you aren't getting married...

Also, Danya Ruttenberg has put together a rather comprehensive overview of many different ceremony options (including Rachel Adler's Brit Ahuvim) on a website. You can find them here. 

The point is, there are options out there if the traditional kinyan, the acquisition of the woman in the traditional ceremony, makes you uneasy...

If you're planning to marry in israel, and are dealing with issues concerning the Rabbanut, there are some organizations that might be of interest to you. There's one organization called Mishpacha Chadasha (New Family) that is working for gender equality under Israeli law in relation to marriage, among some other things. They get as close as is currently possible to a civil marriage in Israel. 

The other one that might be worth checking out is Tzohar. Tzohar works with the Rabbanut, but they try to create a traditional ceremony that is also a spiritual and enriching experience for the couple and their families. Both websites have most of their info in Hebrew. but they're way worth checking out.