I believe you may be either using too much heat for searing, or leaving too much flour on the meat when searing? I sear in batches often, and don't have to deglaze in between batches. You shouldn't have flour at the bottom of your pan, but just enough flour to stick to the pieces of meat. Just make sure you get rid of all excess flour before the meat goes in the pot by shaking the pieces of meat until all excess flour falls down on a plate. In fact flour isn't even a necessity, and to be honest I rarely use it. If you dry the pieces of meat thoroughly then you can sear them without any flour and build your stew with a purer taste that way.
Then remove all the meat and add your onions and shallots over low-medium heat. The onions and shallots will produce enough of their own water to deglaze the pan. If they don't you can always add a bit of salt, which will help them sweat out their water. That means all the flavor from the fond goes onto the onions and the onions are sweated - here again without having to wash the pan again.
I don't add more flour to the mirepoix. More flour gives you a thicker sauce, which is nice, but it also dilutes the meat taste in the braising liquid. Instead, reduce the braising liquid at the end to the desired consistency.
I don't caramelize the onions, I suppose that's a matter of taste, but while I love caramelized onions in other preparations, in a stew I find that it distracts from the taste of the seared meat.
As for the tomato paste, yes, I add it to the mirepoix or onions before the liquid so it can cook a bit before adding the liquid.
Mushrooms and potatoes sound great too. I would personally sautee the mushrooms before adding them in at the end. I would also cook the potatoes separately and add them at the end so they don't give out their starch which would cloud the wonderful stew liquor (the braising liquid).
Hey! I can smell it from here.