Isaacs also advised the reigning Premier Soccer League Defender of the Season to not allow coaches to destroy his career.
Baxter recently revealed that the former Swallows defender faced an uphill battle to win a place in his preferred position of centre-back.
"First and foremost the system that Baxter is playing I think he's favouring a 3-5-2 system," Isaacs tells KickOff.
"You have to ask the question of whether Baxter signed him, or did the Kaizer Chiefs management sign him.
"In his first season, I mentioned that there wouldn't be any pressure on him.
"He played his first season at Swallows, and he got the Defender of the Season award which was brilliant.
"But now people they study you, they see that you are composed and want to dribble your way out of things and that is when you get caught out in your second season.
"But a quality player like Ngcobo hasn't lost his quality overnight, maybe there's something else that needs to be asked as well.
"Is he a Baxter signing or management signing? Does he fit in the system that Baxter wants to play?
"Because if Baxter has better players who understand him and is more experienced because if you look at Daniel Cardoso, he's supposed to be more experienced than Ngcobo.
"Mulomowandau Mathoho is supposed to be more experienced than Ngcobo.
"At the moment Kaizer Chiefs are under tremendous pressure and they need to deliver, at this current moment the Chiefs centre-backs are leaking goals.
"So give Ngcobo a fair chance and try and find a suitable partner for him that can complement him.
"You can't have a so-called experienced player who is busy making silly errors and they are conceding goals through him."
At the time reports suggested that Baxter's original departure from Naturena centred around his lack of influence around the club, especially regarding transfers.
The 68-year-old is believed to have agreed to return with the promise of a more influential role, which has so far allegedly failed to materialise.
An example of this is regarding the recently reported signing of midfielder Siyethemba Sithebe from AmaZulu that was completed without Baxter's input.
Alarmingly Baxter is rumoured to have found out about the Sithebe transfer through the media.
"I was also told when I was at Chiefs that I must leave and I will be put on the transfer list. I need to look for another club.
"But I took that as motivation, I told myself it is every player's dream in South Africa to play for Chiefs.
"I wasn't going to let one coach decide or ruin my dream of playing for Chiefs.
"So he can take what Baxter said as a motivation and grab it with both hands, or he can do the obvious thing and give up."