My old system had both Intel and ASMedia USB 3.0 ports.  Had dropouts on both. 
My new motherboard has Intel USB 3.0 and ASMedia USB 3.1 controllers.  The motherboard has one internal USB 2.0 motherboard connector but it is being used by the Corsair H100i CPU cooler interface.  I have both USB 3.0 and USB 2.0 connections on the BeQuiet Silent Base 600 case front panel but I can't use the USB 2.0 because the Corsair is using the motherboard connection.  I could have installed a second PCIe USB 2.0 port card but I opted to install the Firewire card and use that for my MOTU.  I have one 5 port PCIe USB 2.0 port card but that is being used by my 5 USB connected CD/DVD burners stack that I use for audio CD production (I can burn 5 audio CD's at one time using Nero BurningROM).
 
I have a Toshiba touch screen laptop with Intel USB 3.0 ports (only USB 3.0) and the MOTU does not "play well" with it either.

I can't quote myself, but I have answered my own question - my Sager/Clevo shell has an Intel USB controller.

Hello peoples.
I'm kinda new on the Cakewalk websiter.
I took advantage of the platinum lifetime update deal they had at Christmas.
At the same time, Waves was having a screaming deal on their $4,000 Horizon bundle at $900. They also had the $1,200 Abbey Road Collection on sale for $499. I grabbed both.
It's all running on my Sony Vaio laptop. i7ore 8 thread. 7200 rpm, 8gb ram. Win 7 64 bit
USB 2.0, 3.0, FW.

I have a MOTU midi express XT USB (the new model). It was a bear to get it to play nice with my system. I had its USB 2.0 port hooked to the laptop's 3.0. Motu support said not only do I need to hook it to the 2.0 port on my laptop, but it also needs to go through a powered USB 2.0 hub. It CANNOT be hooked up to anything 3.0. And it WILL NOT be happy just going through the laptop's 2.0 port without first going through a powered hub. Well, it seemed to work.
So now my focus is on either the motu 828mk3 hybrid or 896mk3 hybrid. I would prefer a Presonus 192 studio, but now I'm starting to hear bad things. Both motu models has two adat hookups which can be configured as stereo optical connections, which is exactly what I need. While the Presonus has two adat hookups, only one can be configured as stereo optical.
So it's a toss up.
Motu with two optical but only USB 2.0 and FW
or
Presonus with only one stereo optical BUT USB 3.0

Decisions decisions.

bitflipper
Jim, a general question re USB 2/3...my laptop has both. Except for my external disk drive, I just use whichever port is physically convenient. I don't use a USB audio interface, so we're talking slow devices such as mice and MIDI controllers. If speed is not an issue, is there any reason to make a point of matching USB3 devices to USB3 ports and USB2 to USB2? Power limitations, perhaps?

Just saw this... sorry for the slow response. 
 
Unless you're pushing the bandwidth with the connected peripheral, no... I see no pressing reason to worry about USB-2 vs. USB-3.  iLok and eLicense keys, keyboards/mice, and other low bandwidth (simple) devices aren't finicky about the USB controller.  If you need to conserve USB ports, you can put several low bandwidth peripherals on a USB hub.  If it's just dongles, you can put those on a passive USB hub.
 
Prior to Z77 chipsets, literally *ALL* USB-3 controllers were 3rd-party add-on (as USB-3 was not yet integrated into the Intel chipset).  Similar to using a non-TI chipset Firewire controller, this opens the door for compatibility issues.
A lot of the issues reported with USB-3 and audio/MIDI interfaces are related to this.
Virtually all desktop motherboards have a USB-2 header... so you can add a pair of USB-2 ports for under $10.
With a laptop, you're obviously stuck with what's provided.  If it's recent make (Intel motherboard), you've got Intel USB-3... which generally works well.

I just got the motu 624 and im having a nightmare to make it work with a particular laptop with win 10,4 days i`v been trying in vain.
The funny thing is that it works perfect on a very old pc i have with win 10.
There must be a problem with the new usb 3.0 chipset.
Peace

I just worked a problem on the sevenforums.com help forum. User has a new Z270 PC and his MOTU Ultralite MK3 is having "realtime peaks in Cubase" and intermittent crackle issues with his new PC that only has USB 3.0 ports (at least on the rear I/O panel).  

fireberd
I have an MOTU 896mk3 Hybrid which has both USB 2.0 and Firewire connectivity.  I had two new MOTU 896mk3 Hybrid's.  The first one was sent back and later a second one was purchased (and I still have it).  The MOTU replaced a Roland Octa-Capture that had no problems with the USB 3.0 port so I reused the USB cable from the Octa-Capture with the MOTU.  I would get intermittent dropouts.  With the second one I finally realized I had USB 2.0 ports on the front panel and tried one of those and NO dropouts. 
 
When I built my new PC, back in early December, it only has USB 3.0 ports...

...slightly old thread... updated for posterity.

There is a firmware update for the 896mk3Hy:

896mk3 Hybrid
v1.02 Mac / Win (Release Date 2012-12-11)
Added Windows USB3 compatibility

I have had no problems using my updated unit with USB 2 or 3.

If you're running a newer machine Z77 motherboard or newer, USB-3 is integrated into the Intel chipset.
That eliminates many of the compatibility issues with (older) USB-2 audio/MIDI interfaces.
Prior to Z77 motherboards, literally all USB-3 controllers were 3rd-party.