The first season was okay, but I don't consider it a high point of the series. What was cool about the later Phoenix Foundation years was that they could be about anything. Phoenix had its fingers in many different pies, from government contracts (so they could still do spy stuff) to scientific and environmental research to forensic assistance to the police to charitable and social programs. It made for a very versatile show. MacGyver could go on an Indiana Jones treasure hunt one week and match wits with a Hannibal Lecter-style serial killer another week and try to help an inner-city kid avoid joining a gang another week. Not to mention all the times he got dragged into trouble by his wacky friends like Jack Dalton and Penny Parker. Limiting it just to the spy stuff seems pretty narrow in comparison.
The fact that Eads is now playing a reinterpreted Jack Dalton makes it pretty clear that it's a reboot, not a sequel. Besides, we already met MacGyver's son "Sam" (Sean Angus Malloy, played by Dalton James) in the second-last episode of the show. He'd be in his early to mid-40s by now. Although I suppose MacGyver could've had another son later on...