Other than that Blues boss Steve Tilson had a full outfield squad to pick from for the first time for a while and being aware of the large physical presence of the U's went for a more defensive line-up, Jean-Francois Christophe returning to the side in midfield, Francis Laurent moving more into the centre to partner Lee Barnard instead of the departed Jabi Ibehre.
Far from being the 'fierce and frantic' derby match we were warned it would be the first half was quite leisurly with Colchester happy to play the route one football that manager Aidy Boothroyd is associated with back from his Watford days, and the Shrimpers coping with it reasonably well.
Even so, it was the away side who had the clearer chances, the Blues defence once again making a meal of just clearing the ball out of defence allowing Steven Gillespie a clear sight of goal from only 10 yards out, and he smacked the ball over the bar.
Then an amazing miss. Paul Reid presented with just Ian Joyce to beat, poked the ball past him, but allowing loanee left back Scott Malone to clear off the line.
The best opportunity for Southend fell to Christophe who found himself free at the far post after another excellent Simon Francis corner, but directed his header into the side netting.
Laurent ended his one decent run at the end of the first half with a shot directly at U's keeper Ben Williams.
Then in 12 minutes of madness for Southend the game was lost.
50 seconds into the second period a Gillespie cross from the left eluded several players but found a diving Paul Iffell whose header beat the diving Joyce at close range.
Then, on 57 minutes, the referee was conned by Anthony Wordsworth into giving a free-kick to the away side in a very dangerous position on the edge of the area slightly to the right of the penalty spot.
Wordworth certainly took full advantage by placing the ball beyond the wall and past the fully stretched Joyce into the top left hand corner, 2-0.
The Shrimpers knew they had to get back into the game as quickly as possible and only ten minutes later they did, yet another Francis dangerous cross finding, who else, Lee Barnard, who headed home his 15th goal of the season.
It was all Southend, who then had three great chances in the final 17 minutes, (including four minutes of stoppage time), to grab a point or even more, and missed them all!
The frustrating as ever James Walker, on for Christophe, couldn't control a superb pass from Barnard when he would have been one-on-one with Williams.
Next, Macca decided to take the ball off Barnard's head when a touch from the Blues top scorer would have brought an equaliser.
Finally, loanee centre back Sean Morrison found himself in space with only Williams to beat, but decided to head straight at the Col U shot stopper.
And that was that, the bragging rights to the Farmers this time around allowing yet the Blues only have themselves to blame.
In 48 hours another local derby away to the Borient, another poor result and the players will really have something to worry about, their position in League One.
Southend Player Markings: Joyce - 6, Francis - 7, Morrison - 6, Barrett - 6, Malone - 6, Grant - 6, Christophe - 5 (Walker 67 - 5), McCormack - 6, Moussa - 6 (Scannell 74 - 6), Laurent - 5, Barnard - 6.
Referee: Mr. G. Hegley - 6.