*kohon*
Honestly, TA / Jparser is easy to use but it has the disadvantage of giving the wrong furigana at times. For a Kanji with several meanings, the wrong one is sometimes shown which leads to confusion (specially for someone with zero Kanji knowledge). Whereas in using only dictionary such as JWPce, several choices of the reading (and meaning) of the word are given, which you can choose based on the context of the sentence.
Also, if you are using the Furigana function, it is nearly impossible for guys who are using netbook because it will eat a lot of space on the screen which leads to little space left for the VN. (You may have noticed though, that I'm using netbook.) http://i.imgur.com/HTqLKCB.png
By the way, what do you mean by "hovering"? Is it different from "highlighting the word"? Because I'm pretty sure I said above Upon highlighting a word (in the ITH) that you do not know, the dictionary will automatically search that word って。But if it is just pointing to the word, that's one advantage of the method you are using.
I don't know about the dictionary you are using but JWPce can search Names of People, Places. Furthermore, this dictionary system allows you to add any number of supplemental dictionaries you want to add.
On a more important note, Not using Jparser (using only ITH and any dictionary) has the advantage of forcing you to parse the sentence on your own, which makes you familiar / get used, to the "original Japanese sentence" (not giving any hint on identification of the word / parsing) as soon as possible. Also, not relying on furiganas can let you integrate as early as possible the word in it's original form to its' Vocabulary (meaning) at the same time since you are focusing only on the original word in Kanji.
In the end, it's a matter of choice. I just gave people "one more choice" in reading VNs.