The Smartgun is an excellent generalist weapon. At the point where you can get it (mid 1998), and in every specific role, there's probably a better weapon, but the smartgun is probably the 2nd or 3rd best. After you get a steady source of alloys, the Tritanium ammo upgrade also keeps it relevant.
It won't be able to deal with the toughest enemies (it can still hurt the Supersoldier from any angle with a lucky roll), but it works well against most opponents at most ranges. In a previous game of mine, it was the leading cause of deaths for my tanks (due to friendly fire), so it definitely can pierce pretty heavy armor.
The main strength is its volume of accurate fire: 3-round snap and 5-round burst with a range of 25 each, and you can fire them twice and still move. The macro SMG doesn't have the rate of fire or range, despite doing a bit more damage.
Of course, I do supplant the Smartgun with sniper rifles and explosives to deal with opponents it's not good against.