The pitched roof will make the house cooler and will provide additional storage area between it and the flat roof. Both roof types come in many styles and colors. Metal is more fire resistant than composition or wood roofing and can be applied more quickly. Metal roofs can usually be installed right over the old roof. Some are guaranteed for 50 years or more.
Metal roofs are more expensive and are easily damaged if walked on incorrectly.
The longer-lasting shingles are thicker and their shaped appearance makes a more attractive roof. The problem with installing siding, particularly vinyl siding, over wood shingles or other wood siding is that it does not breathe, while the wood underneath does. That causes the wood underneath to absorb moisture and ultimately decay. You would be better off to strip the shingle siding and repair any damage, or add additional bracing, before putting up the new siding. Generally, three layers on a roof are the maximum.