You raised some good questions. The correct answer is composites are application dependent. The aspect that I like most about composites (advanced composites - elevated temperature/pressure - mainly fiberglass/graphite) is their ability to fabricated strong, compound contoured parts simply, reliabiably, repeatibly, and with good process control, meaning high quality. Many factors affect the decision of which techique is right; part quality, cost, strength, volume, etc.
The hand layup/vacuum bag/autoclave technique is excellent with pre-preg materials (fiber and resin content are controled) but the materials and process equipment can be expensive and the material requires refrigeration when not in use. Generally low volumes of parts are produced using this method making them costly so high volumes are recommended to ammortize costly labor and tooling. If 'dry' fabric or toes of materials are used you are working 'wet' (refering to resin) then you have more of a potential for resin rich or starved finished product conditions which would significantly reduce the parts strength. Working wet can be messy and has more health concerns if proper engineering controls are not in place. If a RTM (resin tranfer method) is used and refined working wet can be performed with great repeatiblilty on relatively complex parts. Variations of RTM (VARTM and SCRIMP) exist that make wet even more conducive to better quality and less cost. Filament winding and toe placement with either prepreg or wet can used but each has it's limitations in volume, cost, quality.
Room temperature/vacuum, prep-preg/wet material curing composites are an alternative but have service temperature/strength limitations.
For most high strength applications thermoseting resins are prefered as a matrix material but thermoplastic resins are also increasing in use. I can comment confidently on most other composite applications and manufacturing issues but will leave that for another response. I hope that this addresses at least some of your concerns.