I am completely in favour of the rotation, but as far as I can tell, these are the arguments against it being a good thing . . .
1. Players will be losing valuable cards sooner than they expected. Some people have only just got their hands on Luxray and Uxie X etc.
Answer: Long answer, so I am breaking it up.
a) It was rumored for what, at least a month before an official announcement was made they were considering it.
b) It was officially announced they were considering it what, one or two months before they actually confirmed they were.
"a" and "b" means sellers, traders, and even normal players all had enough warning to sell/trade off their inventory of the cards rotating out. A random player who just got a hold of it will still be able to enjoy it for casual play, and indeed this is probably why they just got a hold of it. If someone is willing to pay top dollar for cards to use just for Pokemon League and can't keep abreast of current developments happening this slowly, it really is their own fault.
2. There were easier ways to fix the format - ban certain cards or not bring in the B&W rules
Answer: Neither of those are easier in the long run, and the former isn't even easier in the short run. I can go into detail if anyone actually wants me to, but I was on my fourth or fifth paragraph detailing it before I decided to just post these two sentences!
3. People who earned their Worlds invite playing MD-on decks should be able to play MD-on decks at Worlds
Answer: Why? Is there a formal contract between Pokemon and the players stating that? If there is please tell me! Otherwise this is a "squishy" emotional argument, not a logical one. Players worthy of going to worlds should be able to adjust, even on a budget. Evening winning a trip and invite, someone truly flat broke can't afford to go.
4. MD-on was not as bad as people make out - Sabledonk didn't dominate BRs, donks are part of the game etc
Answer: Completely subjective. This is an opinion even if it is supported as facts. I would argue the format is worse as it still isn't enjoyable even when Sabledonk didn't dominate the format. I would point out that "donks" are part of the game, but decks built entirely around the concept and winning entire tournaments is not supposed to be.
5. The relatively late notice hurts people who are not able to playtest much/get new cards before US/CDN Nats. They will probably end up just netdecking something with Emboar in it.
Answer: So in short they didn't deserve their invite then in the case of play-testing and resorting to net-decking. Plus, even if the format hadn't changed this statement holds true unless there are no new cards introduced during the season! A single card can change the format just as much as a set if it counters something commonly played and heavily relied upon.
6. HGSS-BW will centralise around a few decks and will be dominated by a handful of archetypes, just like MD-on was
Answer: Even if this is the case, at least they should be newer decks and be a result of the time allowed for preparation and smaller card pool. Of course, this it not the case yet and will only really be known after the tournaments.
7. The card pool is too small - less room for creativity, and lack of draw makes format slow and frustrating
Answer: Again, opinions even if based on facts. Given what happened with MD-On many would argue that the current card pool was too large, resulting in unintentional power plays as cards never meant to be legal for Modified play interacted with one another, especially under rules revisions meant for the later cards. This in turn restricted creativity as deviating from the standard patterns meant your deck failed.
Otherwise, some of us prefer a slower format and find the "faster" MD-On more frustrating.
8. There is no legal Glaceon in Modified any more
Answer: I know this was probably a joke comment, but just in case here is a serious answer. This is a common problem at the beginning of a format, and I doubt Glaceon is alone in being missing. Given time it solves itself. 
