Has your architect not been able answer your questions?
Vinyl cladding has previously had problems with dark colors fading and expanding too much in direct sunlight. I don't know what they have done to resolve that problem but I remain skeptical. Andersen is the only major manufacturer that uses vinyl cladding and I don't like many of their other details and features.
I have never actually seen a fiberglass window and have avoided them because of their low budget details and features.
If you use an aluminum clad window avoid Pella. The aluminum work is terrible.
What kind of wood windows were specified? They should be cheaper than clad windows if you add the cost of field-applied trim to the clad windows. If your contractor hasn't given you this cost separately you cannot know which system is cheaper. Make sure he includes all field applied sealant, backer-rods, trim, extension sills, and labor. You will be surprised at the cost. All of this is already included in the price of the wood windows.
I used Eagle windows with wood frames/casing trim and aluminum clad sash (best of both worlds) until Andersen bought them and the glazing stops started leaking on one of my jobs. Norco makes a reasonably priced all-wood window.
I have been designing buildings of all kinds and sizes for a very long time and now refuse to add casing trim over nail-fins in the field. In addition to avoiding unnecessary personal liability and a big hidden expense, I avoid a joint detail that is hard to seal properly, especially at the sill. Most manufacturers require a backer-rod at the joint, which is what the sealant manufacturers insist on, but I have yet to see one used. Eventually, the improperly formed sealant in such a narrow deep joint fails even though you can't see it and water is drawn into the joint by capillary action. It is hard to imagine how much water is drawn into a fine continuous crack unless you have seen it yourself and I have seen it many times. Then the nail-fin becomes the only window flashing which to me is an unacceptable detail. Water that gets behind the fin cannot drain out at the bottom because of the bottom nail-fin. The sill detail is even more difficult. If the sill does not slope and project enough a wood sill must be added or water will roll over the sill and pass behind the siding after the sealant fails if it ever worked in the first place which was the case in a dispute with Andersen over this detail. Fortunately I was a consultant for the owners and not the designer of the project. Don't ever accept a flat short sill!
On a factory-trimmed window, the trim to frame joint is glued and stapled and is so strong and permanent that the window is only attached to the building through the trim. I flash the rough opening jambs and sills with Ice & Water Shield membrane so if water gets behind the trim it can drain out below the sill. Some contractors prefer metal or PVC sill pan flashing which is fine too.
I don't know where you are located but Boston Sash in No. Dighton, MA makes the best inexpensive window on the market. It is a copy of the Marvin EZ Tilt with compressible PVC jamb liners and I have used them in multi-million dollar houses. It even has a pulley balance system and tilting sash. The glass is putty glazed by hand and they offer no cladding but they offer a cedar or cypress sill and any kind of wood or synthetic casing trim. You can even supply the rough trim or sill material to them yourself. These windows are a bargain! They even make a historic replacement sash with the balance hidden in the sash edge. They are a small company and only sell through lumber yards.
http://bostonsash.com
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