I doubt so. The pyramids were deeply linked to the lore of DOS1 and the Shelter Plane at the End of Time.
But I personally think it's good that they're gone anyway. Pyramids (especially combined with teleport magic) made many puzzles way too easy and severly limited the general world and puzzle design.
Teleporter pyramids were in the Divinity series for years before OS1 was even developed, so that's not a reasonable reason to exclude them.
And I wouldn't say they made the puzzles easy. Rather, the puzzles were designed with the pyramids as a solution and were simply not very difficult puzzles, period.