Q:

Is the current Bitcoin implementation easy for different users to participate in a single transaction?

I read a paper from 2013 (Androulaki E., Karame G.O., Roeschlin M., Scherer T., Capkun S. (2013) Evaluating User Privacy in Bitcoin. In: Sadeghi AR. (eds) Financial Cryptography and Data Security. FC 2013. Lecture Notes in Computer Science, vol 7859. Springer, Berlin, Heidelberg) that, regarding transaction input, "currently, Bitcoin clients do not provide support for different users to participate in a single transaction; to achieve this, users would have to modify the Bitcoin client implementation themselves". 
What about now?
Also am I correct that most of the transaction nowadays have still only one user as input?
Sources (to ex. papers) would be nice.

A:

The referenced paper is from 2013. It may have been true that at this time it was difficult, to share a spending activity amongst users. This link here https://gist.github.com/gavinandresen/3966071 explains the details around multisig, and comes in early 2013. As of today, you got it correctly, we have multisig in two variants, and the statement doesn't hold true anymore. 
On the aksed sources: there was a paper from 2014 (http://www.quantabytes.com/articles/a-survey-of-bitcoin-transaction-types), that evaluated the distribution of transactions type, but that is the last I know of... and I haven't seen any updates since then. 

