I currently run the LSS2/skimmer, but am thinking of changing to the totalscan. Any pro or cons with either on. I am running an HDS 9 Gen 3.

Thanks

I just switched to TS because of a trolling motor change. Personally I see no difference.

Biggest con will be loss of high speed sonar readings.

On drivers side I have a HDS 9 Gen3 with TS mounted on roof of hull step and also a HDS 8 Gen2 with a transom mount skimmer transducer.
Use the Gen2 mostly for GPS but sometimes also 2D sonar..

TS works great. It's a little deeper in the water than the skimmer and the TS is at least as good if not better at high speed than the Gen2's skimmer

I would stay with LSS2 assuming it is working & you have a separate sonar transducer that is working well. If you move up to Carbon or Live units, go with new Active Imaging SS ducer.

I think the TotalScan is required if you want to use SonarCharts Live with Navionics. Probably no other benefits if you already have a LSS2 and separate skimmer on your transom.

I personally don't even display sonar while running so the loss of 2D at high speed was not a issue for me, and I have a thru-hull I can switch to if I absolutely need it.

This.