Defenders Taina Nauga (GK) and Talitua Leo (GD) were gutsy but just not enough against Manawatu's tall shooters.
Next up was Auckland and a couple of tough umpiring calls went against Blue in a 35-32 loss.
An injury to Nauga saw coach Ora Nyman move Leo into goal keep, shuffling Kristin Thompson (GD) and Keilani Tyrell (WD) with Rebecca Tamati coming on a centre.
"The new combination kept up with the tall physical Aucklanders and we had the crowd behind us as the score got closer," said Nyman's report.
"Two controversial calls from the Auckland umpire saw Wanganui finish three behind.
"Ironically, the Auckland Umpire was moved to the C Division the following day."
Blue then faced pool leaders Howick Pakuranga in their last Sunday game, losing 39-26 after being in touch at 19-15 by halftime.
Midcourt breakdowns saw Nyman swap Tyrell (WA) and Kiana Millar (C) around and bring Sarah Gower-James to wing defence, but they took time to settle as Howick stretched the lead.
Monday saw Wanganui cross over to play the Auckland Year 9s and go goal-for-goal until the third quarter, losing 43-34.
Flower motivated her team and by half time Blue was only two goals down, with the attacking end sublime as Flower and Aki were continually in tune.
Leo (GK) and Tyrell (WD) hustled the Auckland attacks well, but by the end of the third quarter the Blue midcourt was struggling with the tempo and physicality.
Second game on Monday was Thames Valley ,who had beaten Manawatu earlier, and Nyman said her team dug deep to win 41-35 in a season-best effort.
"Shooters were accurate and fluid, midcourters punched fast and timed passes well while the defence continually turned over ball, we just didn't do anything wrong."
On goal differential, Blue missed out on the middle range of the grade and went into the playoffs for 12th to 16th on Tuesday.
They face Waitakere 2 and despite their opposition having a 6ft tall goal keep, Flower and Vaiao-Aki continuing to shoot accurately.
Gower-James came onto wing defence in the final quarter made three crucial turnovers to ensure a 38-25.
That set up the final game, again with Thames Valley, but fatigue had set in for an eventual 43-40 loss.
Nyman credited Flower, Vaiao-Aki, Leo and Tyrell as the pivotal players.
In the C Grade, Wanganui White started Sunday very well with two wins against Hamilton City Development (34-24) and Invitational Yellow (34-26) after good defensive work by Teagan Tapa and Leigha Stormont, while Maggie O'Connor provided good ball for shooter Kara Adrole to convert with ease.
The day's last game was not so easy with fatigue setting in as White had a heavy defeat to Waitakere Y9 37-20, although they still secured a spot in the top 8 of the grade.
On Monday they took on top seed Waiuku in a real nailbiter as White forced the favourites to make changes every quarter, but could not finish off in the 32-29 loss.
They then faced Wairarapa, a rival from earlier in the season, going down 34-30.
Competing in the 5th-8th playoffs on Tuesday, White met Matamata first up, going down 39-38, although Piper Neil had an outstanding match.
There were some tired bodies for the final game, another narrow loss at 31-27 to Hamilton A.
Coach Janine Plumridge and manager Malissa Mahoney were thrilled with the overall performance of the team, captained by Teagan Tapa.
Team mates were O'Neil, Leigha Stormont, Cori-Lee Herewini, Maggie O'Connor, Mikayla Heka, Te Whetu Matthews, Katarina Rawiri, Maze Thompson-Koro and Kara Adrole.
