We delayed our kids' vaccinations by a year or two (or more in a couple cases), particularly after our oldest daughter seemed to have a bad reaction to a DTaP combination at a young age (I can't remember for sure but I think she was under 1). She got very sick for over 6 weeks after that shot, and I'm convinced it did something to her system long-term that affected her immune system and overall disposition and health, because there was a marked 'before' and 'after' effect. Our daughters were all small babies, and I think that waiting till they were bigger (after that initial mistake) was a good decision.
In any case we delayed the shots and also spaced them out so that we weren't giving multiple shots simultaneously. You should know that even though the common practice is to give shots by the threes or fours in some cases, you can request that they be given individually, if you think that may be easier on your daughter's system.
We were careful not to give them when the girls were sick, either.
In some cases, kids this age, in this location, have little to no risk factors at all for getting particular diseases. Our kids have absolutely no risk factors for getting hepatitis B at this age, so there was no reason to rush that one, for instance. THat was one we delayed.
We also did not give them varicella or some of the newer, 'optional' vaccines. Our youngest is 3 1/2 now and she hasn't had any problems with any vaccines, and she's up to date with the exception of the optional ones. Our oldest is 13 and I probably will have her do the Gardisil vaccine in time (protects against HPV) - but I'm watching the literature about this in the meantime because it's such a new vaccine. The lack of long-term data concerns me about many of the newer vaccines.
I you are wise to be careful about this issue. As far as telling your doctor, I think the best thing is to very matter-of-factly state that you are going to space out the vaccines so that your daughter will get them, but not all at once and not as early, in some cases. The doctor should absolutely respect your decision. It may make sense to do some vaccines earlier than others, such as the DTaP (or you can actually get them separate, if you insist), because pertussis does go around, and the vaccine can lessen its severity. Personally I am not a strong supporter of that particular vaccine, but what I'm saying is that the doctor may have sound advice about the order or importance of one or another based on disease trends occurring in our area.
If your doctor gives you a hard time about delaying the schedule, it may be time to find a pediatrician who will respect your wishes and work with you -- there are plenty who will (and plenty of moms here can recommend their docs, I'm sure).
By the way, another related thought - the flu vaccines are by and large not helpful because the vaccines are developed months before it is known what strain of flu will emerge. If you think someone may have the flu, the best thing is to go to your doctor immediately and get tested - it's not a pleasant test, but if he or she tests positive and it's within the first day or two of symptoms, you can all take Tamiflu, which is very effective in preventing and reducing the severity of the flu.