Mokwena returned to Sundowns this week after spending two-and-a-half years at Pirates as both an assistant to Milutin Sredojovic and head coach.
The Sea Robbers managed to challenge for league honours when Mokwena was sitting next to 'Micho' and 'Dukuduku' believes they were on the right track.
"Eish my brother, I believe Rhulani was building something at Pirates, I thought he was our long-term plan," Makhanya tells KickOff.com.
A disappointed Makhanya hopes one day Mokwena will return to The Buccaneers because his mission was not complete.
"I'm not happy, I wanted him to stay," Makhanya admits.
"He is a very hardworking and passionate young man. I feel he was about to change and benefit the club. I hope there is no bad blood because I still believe one day he will return and finish what he started."
Scroll right to see Makhanya's Bucs-heavy Dream Team (4-4-2)
GK - Thabang Stemmer - Good reader of the game, organiser, good shot-stopper, good positioning skills, good on penalties.
RB - Jimmy Tau - Leadership, comfortable on the ball, good game-reader, good at one vs one situations, overlapped very well and good crosser of the ball.
LB - Abednego Netshiozwi - Strong at one vs one, comfortable on the ball, good overlapping skills.
CB - Lucky Lekgwathi - Good leadership qualities, good speed, good header of the ball, good at one vs one situations, hard tackler.
CB - Fabian McCarthy - Clever, good game-reader, organiser, calm and comfortable on the ball.
CM - Ernest Mtawali - Classy good game reader, had the ability to defend and attack, could score goals from far, comfortable on the ball.
CM - Benedict Vilakazi - Ability to defend and score goals, good game-reader, creativity, ability to use both feet.
RM - Steve Lekoelea - Had speed, good at one vs one, ability to cut inside and good crosser of the ball. He was also a good set-play taker, creative, not a one-dimensional winger.
LM - Helman Mkhalele - Great speed, good one vs one. Ability to cut inside and connect with other midfielders and strikers. Scored and created goals, and a good crosser.
ST - Benni McCarthy - Could score goals!
ST - Lesley Manyathela - Technically gifted, always within striking positions.