Found the answer here:
WMM on both clients & AP seemed to correct the issue. The range isn't the best.
I guess not, but just have a try!
Thank You Everyone for help! I bought new router and my problem was gone without reinstalling windows or configuring something... 
Having EXACTLY the same problem, n6300 ultimate with linksys E4200, getting max 54 mbit, when N mode disabled in the router setting i am not able even connect to the router. 54 mbit max on 2,4 ghz as well as 5 ghz, i´ve tried multiple different settings without result, using the latest 15.1.1 firmware. Starting to be desperate 
Is it realy compatibility issue??? I´ve seen some threads where people reported they are using 6300 with linksys e4200 without issues...
I have the same issues with my ThinkPad T520 which comes with a n6300. Too bad Intel did not come with a fix or answer on this themselves.
Well the good news is I seemed to found the solution.
By changing some settings on the Cisco E4200 I was able to FIX it. Windows 7 now reports 405 Mbps
I am currently using the Intel drivers 15.2.0.19 and on the Linksys I installed the Tomato RAF custom FW version 1.28.
Configuring the Intel and E4200 as stated on previous posts did not solve it but I changed on the E4200 the Bluetooth Coexistence on both 2.4 and 5 Ghz to Preemption and it worked!
