The Magos Prime is exactly what the name suggests he should be. The primary mechanicum person to go to. They are a high adept of the Cult Mechanicus and have more than likely travelled significantly down the road of replacing most parts of their flesh with cybernetic and robotic replacements. In the extreme cases, their organic remains are contained in cages that are very reminiscent of Dreadnought chassis.
The strength of the Magos Prime is dependant upon how one goes about building them - and indeed the army around them - to a great extent. Will you be going for a close combat Magos that is armed to the teeth and has a jump pack? Or a more ranged Magos who is likely to stay in place and shoot off a conversion beamer? Or more of a support role? It all really depends.
Their stat line is not great - particularly in comparison to Space Marine Legion commanders and the like. They really need to think clearly about their battle field role and play to their strengths. They also need to think about how to NOT give away "slay the warlord" and similar victory points to their opponents. A 3+ armour save is an issue though (unless upgraded to an archmagos -- which you should be doing for all options listed below… I've not done this on everything just to be illustrative though).
I want to give one suggested build per Orders of High Techno-Arcana. Each Magos must choose one of these orders, so I figured an example of each would be productive.
Archmagos Prime, Archimandrite Order, djinn skein, 4 cyber occularis, servo arm, Graviton Imploder, Chain Fist (295 points)
This build is over the top, and is an all-comer build. It is meant for tank heavy armies wherein the commander will be riding with his troops. His weapons are designed to be able to take on most things in the game short of primarchs so as to stand a threat to almost anything. Team up with lots of tanks and a quality squad to do some real damage.
Magos Prime, Malagara Order, rad grenades, power fist, jet pack (160 points)
The monster hunter!
Magos Prime, Myrmidax Order, 1 conversion beamer, 2 phased plasma fusils (185 points)
With hatred of everything coupled with precision shots, this guy really can really ruin someone else's day unless he is taken care of.
Magos Prime, Ordinator Order, jet pack, melta gun, melta bombs, chain fist (150 points)
This is the guy that goes to hunt tanks. Use the orbital bombardment early for goodness sake though.
Magos Prime, Lachrimallus Order (120 points)
A cheap HQ selection that would befit a totally cheap army that is based around adsecularis units. Many many bodies on the board here, and we're saving on points with the HQ to ensure even more bodies.
Magos Prime, Macrotek Order, corposant stave, machinator array (145 points)
This is a support choice that also opens up the possibility of having more than one fortifications available. Add in some nastier weapons and melee selections to taste.