The 21-year-old England international has found himself cast in a series of different roles so far this season as new manager David Moyes attempts to find a winning formula, and has suffered some difficult spells with United struggling to find their legendary consistency at times.
Pallister is convinced Jones would benefit from an extended run in his favoured central defensive berth, but believes his versatility means he may find himself continuing to shuffle his way around the team.
Pallister, who was supporting the Manchester United Foundation Chevrolet Trax eBay auction, said: "He has played in midfield as well and he's played right-back.
"I feel sorry for Phil in that respect. It's not very conducive to finding your best form if you are being put in all these positions.
"I certainly wouldn't have liked to play right-back or centre-midfield or anything like that when I was playing centre-half.
"You find a rhythm when you are playing there week in, week out and maybe that's something he has got to contend with, the fact that he is decent in other positions as well and sometimes, the squad has to be utilised like that.
"I am sure he would prefer to sit there in the centre-half position and play week in, week out, but unfortunately that's not going to be for him at the minute."
The reigning champions have endured a mixed start to the season which has left them sitting in eighth place in the Barclays Premier League table having lost three of their 10 games to date - to Liverpool, derby rivals Manchester City and, most unexpectedly at Old Trafford, West Brom - while they needed a concerted fightback to prevent Stoke repeating the feat after they twice took the lead as the away team.
United lost only five league games in the whole of last season, and their recent difficulties have catapulted Moyes' defence into the spotlight.
Pallister accepts that Rio Ferdinand, who celebrates his 35th birthday on Thursday, and 32-year-old Nemanja Vidic, who has had injury problems in recent seasons, cannot play every week, but is confident that a new generation of defenders in Jones, Chris Smalling and Jonny Evans have the talent to step into their shoes.
He said: "He [Moyes] is still trying to probably find out which is his best partnership.
"Rio and Nemanja started the season and we conceded some bad goals - not always down to those two in particular, the team as a whole has got to defend.
"But Rio has certainly been out of the firing line for a little bit and Nemanja has come back in recently.
"I think Rio is going to be handled in much the same way as Ryan [Giggs] and Scholesy [Paul Scholes] in terms of he won't play every week because he's 35 now; Nemanja has had a serious injury, he probably won't play week in, week out.
"But we have got plenty in there with great players like Chris Smalling, Phil Jones and Jonny Evans, who I think has been outstanding in the last year, and I think he has got a shout to be a permanent fixture.
"As I say, he is still trying to find out which is his best pairing, but I have got no doubts that we have got the quality of players who can settle into a back four and make it stronger."