Hi,
I have a 4 years bach degree from India
I did masters from USA in electrical engineering and while doing masters, I worked as a "research assistant" for 1 and half years ( 20hrs a week).

I worked for 2.6 years in IT field before joining my current employer.

My employer says I need to have 3 years experience + Masters before joining the company in order to apply for EB2.
I would be completing my 3 years of employment by April 2009.

My employer advices me to apply in EB3. Should I take risk and apply in EB2? Because I don't qualify the 3 years experience rule, what are my risks here?

Can the research assistantship be used towards employment evaluation?
The experience in assistance ship is similar to my current job experience. But my employer says he can not consider that, as my job title was "research assistant" which would categorize as a junior position.

I like my employer and want to stay here. At the same time, I want to apply in EB2. I would request you to please let me know my options.

Did both of you consult the attorney?

Be sure you are not confusing the employers requirements for USCIS requirements. The masters degree for the EB-2 can be met with bachelors plus 5, but you want to be sure you qualify. See the company attorney to be sure, you don't want an EB-2 labor certification approved and then denied at the AOS stage. Good luck!