For starters, if you use only default Apple apps and expect the most seamless integration, then Preview is your best bet as it integrates nicely with Safari. However, since I use Chrome, I really don't care about that.
For this comparison, I won't be discussing the full feature-set offered by these PDF viewers but rather only those features that are of interest to me - specifically search accuracy and functionality.
My test doc will be "Brocade FastIron_07200_ConfigGuide.pdf", a technical document of 1,854 pages.
Test 1 (search for the string "link-aggregate"):
A search bar and pane is oriented on the right side of the window.
There is a single means of searching - cmd+f
Preview begins searching in real-time as the search string is entered. There is no indication (e.g., status bar) of how long the search will take but there is a spinning wheel icon.
My search took 38 seconds and yielded hits for 9 Pages.
Preview doesn't say how many actual hits there are for the string in question but lists how many pages contain the string.
Adobe Acrobat Reader:
There is no search bar pane by default. There are (2) types of search.
1) Cmd+f launches a small blue pop-down search bar. Search values entered here are displayed one-at-a-time. Move forward using cmd+g and backwards using cmd+G
This is not that useful when searching a huge document because it offers no context of where the result is nested within the entire doc.
2) Cmd+F launches a separate advanced search window for an indexed search. The actual search is only run after the search string has been entered and "search" is clicked.
What's nice about this search is that a pop-up window will appear listing a progress status bar.
The search took about 19 seconds and the results, IMO, are far more useful than those yielded by Preview. Here we have 35 hits for the string link-aggregate.
Skim has the search bar located in the left pane over the Table of Contents. Like Adobe Acrobat Reader, there are (2) ways of executing search - cmd+f launches a pop-up window for line-by-line results whereas entering the search string in the search bar will yield a search index.
The search commences in real-time as the user types and displays a progress bar (on lower righthand corner). The search yielded 30 hits.
Preview is my least favorite. Search results, as displayed, are not as useful as Skim and Acrobat. Preview supports bookmarks.
Adobe is fast and accurate - a great research tool. Adobe does not support bookmarks although the Comment/Sticky Note features can be used as a pseudo-bookmark system within the local document.
Skim is accurate and with a fantastic interface. Skim supports bookmarks.
Currently I am using Adobe Acrobat Reader since I like having a large, separate window for searches. However, Skim is an excellent app that was my default PDF viewer before enhancements to Acrobat made it more competitive.