The engine/transmission combos are not robust enough, little durability issues, and Ford not stepping up to the plate for service after sales. The F-Series is probably very good for a recreational buyer, but the commercial market is learning it's not as good as the GMs for heavy duty or chassis cab usage. Their Power Stroke diesels still have some issues, compared to the Duramax/Allison transmission in the GM. Part by part, I'm convinced the GM full sizers or medium duty C4500-5500's are designed to last longer and be more robust than the F-150-550 no matter the truck application.
Dodge is slowly coming up to bat and will get more and more serious with their trucks. They are branching into more segments of the truck market more seriously. In some places, they are certainly standout.
Combined sales, GM still sells more units than Ford, although Ford does very well. And overall, I think GM is the one to beat.
You are mixing up a little your truck categories. You can't compare a C5500 with a F550. C5500's competition is the F650 (both up to 26,000 lbs GVWR). And the Ford F650 offers Cummins and Caterpillar with Allison trans. Cummins is not available from GM. And if you're playing in this category, Cat or Cummins are more appropriate, IMO, than the Isuzu of the Navistar engines. Unless GM has changed its frame in past few years, Ford's used to be significantly stronger.
GM C-series compete with Ford's commercial truck F650/F750. The F150-550 are not commercial trucks, per se. GM has a big problem because they have nothing to compete with the F450 and F550. So they released a "lighter" version of their their commercial trucks and created the C4500 & C5500. It is probably an overkill for the GVWR class of 16000-2000 lbs GVWR.
I beg to disagree with you. When it comes to work horses, Ford trucks have a better reputation than GM in the fleet world. I was always told so by people working in the industry. I will give you the Duramax engine with the light duty Allison trans is a very, very good powertrain for the 2500-3500 chassis cabs and pickup trucks. Ford is working really hard in improving the last Powerstroke engine and is very involved with Navistar to resolve the engine issues. That Isuzu is a real sweet engine indeed.
That said, both Ford and GM need to check in their review mirror and watch Chrysler...