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Thanks! Well I would not think this abnormal if it was a shift between a few position.. Even to 25.. But as an example today i have had about 20 KW out of my list of 150 that went up 197 positions EACH back to their regular or better 2-6 ranking then  I have another 40 KW that are still further at a ranking of 200 or further. Every day is about the same yo-yo effet. I do see a general drop as well with some KW that slowly went down the 25.. So it feels like I am getting hit by some kind of weird randon update. But I am also wondering if this has to do with my ranking tracker.. Organic traffic is down 47% to LY for march...  I am trying to get it better, but it is hard to keep track of progress with such variations.. Id love to hear if anyone knows more about this case..

It seems like you are taking the correct steps. I'm guessing those pages were tossed in to the supplementary index (as they were most likely were dupes) and I beleive by tweaking your robots.txt files, over time, these should be removed. Another thing to do is inform Google on what to do with those parameters inside webmaster tools: Configuration => URL parameters

whether or not it's advisable for ranking purposes to noindex any page with mostly 'stock' content, and only allow Google to index hotel pages with unique descriptions? This is what I would do. In the past you could allow those pages open for indexing and google would simply ignore them.  Now you run the risk of hitting a Panada filter that will reduce the rankings for the rest of your site. Good luck in this niche.  Really really difficult.  You need either enormous site strength or lots of unique substantive content (which you are doing).

Thanks Donnie. Yes, I completely believe that the right attitude is what you are talking about above. I guess I am just trying to understand the rhyme and reason to it all because, while I believe in the long term it is not all about SEO, and it is more about the user and their experience (and conversion!), at the end of the day, they are not especially following that motto and yet something is working in a very strong way for them. So while I fully intend to apply the best to my own work, I do want to understand the reasoning in what I am doing or not doing, and the whys of the result I am and will be getting. Basically figuring what the "good" is of what they are doing  Somehow it is taking me a while LOL

If the links are exact anchors (which I assume they are if you were doing link exchanges) and are in the footer, I would get them removed. I have not heard of anyone linkbuilding their way out of Penguin; only by removing bad links have people recovere. So yes, I would remove these links if they are this way. Branded links are usually fine, unless they are something like what WPMU dealt with and they were too close to exact anchors. Penguin seems to mean that there are specific links that Google does not like. Go look at the posts that have been written for the different types they don't like, and look through your backlink profile to find the money terms where you might have too many exact anchors. Good luck.