Hiya, thanks for taking the time to answer my comment!
I'm in the process of building a multiphoton microscope (donated axiovert 135 body and Hamamatsu detectors). Of course, I have nowhere near the amount of money to buy a Ti:Sapphire and would much rather spend the money on good IR lenses and upgraded optics.
I've been looking at "alternatives" in the form of Ytterbium based lasers for the reasons you describe: small 2 box footprint (with a pulse picker), integrated solid-state pump and no cavity tuning (or so the manufacturer says). Other advantage is the reduced photodamage with a two photon excitation around the 1030nm mark, but I am still waiting for an answer on the expected second harmonic / third harmonic signal generation efficiency (probably something I won't find out for certain until the entire microscope is built). 1-5% for THG seems frighteningly low, but fortunately, the detectors I'll be using have low dark count.
Also the 5nJ per pulse spec from the manufacturer worries me slightly. One thing I haven't quite worked out from the available literature is the discrepancy between the available energy (say 60-100nJ per pulse from a Yb:KGW laser) and the energy deposited on the sample (around 1nJ per pulse, when mentioned). I hope the loss comes from using a neutral density filter and not from losses due to the microscope optics...
With the right skills of course, the whole process of building your own microscope seems easy enough :-)