I've been playing for 4 years, but didn't REALLY get serious about playing until about a year ago. I play bass and guitar, and I guess I'm pretty mediocre at both. I'm gonna start jamming with a couple of guys pretty soon who know what they're doing in an indie/alternative kind of band.

I know the blues scale, natural major and minor scale formations and can play them with relative ease, which has helped my improvising.
When I play bass, I use my knowledge of fifths, thirds, etc. to spice up my bass lines, but I still feel as if my guitar and bass playing is really stale. I know the names of most of the notes on the E and A string off the top of my head, but it takes me a while to figure out the note names on the rest of the strings. I also have a pretty good ear, so I can listen to a bass line and figure things out pretty well.

I also feel as if me playing guitar for so long has negatively effected me as a bass player. I feel like my riffs are more melodic based and don't compliment the groove or rhythm as well as they should.

I want to get better, but I don't know where to start, what to practice, how long to practice, etc. Does anyone have any suggestions? Any would be appreciated, I'm trying really hard to become a better bass player.
You know when you're playing a relatively easy rpg and you reach a certain level, say 60, when you realize you could blaze through the rest of the game without anymore grinding? That's where you are. The thing that seperates level 60 from level 99 is technique and experience. The next step would be to learn new techniques (pop and slap, tapping, strumming, etc.), learn the modes of the scales and when to use them, and practice (with and without other musicians). Practice everything, scales, chords, arpeggios, spider exercises, new techniques, everything. But I'll tell you ahead of time, no matter how good you get, you'll always feel like you're level 60. So don't get too downed about not progressing as fast as you'd like because as long as you're trying to become a better bass player, you're not mediocre.
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Thanks for the encouragement, I'll make sure I'm more optimistic about my playing. Are there any online tutorials (videos, websites, etc), that people have found to help them the most?

Also, I think my biggest problem is utilizing the entire fretboard when I'm playing. I really only use the minor blues scale to improvise, and feel as though I'm very limited as to what notes I play.
I feel your pain. I know a bit of theory, but I mostly write my own material by thinking of it, and then finding the notes and sometimes just by messing around and seeing what I find. This methid works for me but it means I have very little improvisation skill, because I'm not fluent in the language of music theory. Anyway, you don't have to feel annoyed or anything like that, you probably know more theory than Flea!

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learn how to arpeggiate chords, that will help you support the band and fill up more space. Also buy some sort of rythm book if you need help commin up with rythms. Practice syncopation.
Buy a drummers syncopation book (reffered to previous post) and practices the drums rhymths but adding notes instead of just doing one sound, so you have a clearly plain road in front, its up to you to paint it c:

Since my brother is a drummer i did this and oh boy did i get better lol... DUH!!! Its a really fun thing to do c: and its pretty good for your playing too.

Also playing guitar and bass at the same time wont compromise the other as long as you put yourself into it, im most of the time on my guitar composing and when i come back to my bass i do it just as good as i should. Just focus and correct practice will get you bettah c:

Check a band called Maximum The Hormone, thats some crazy stuff, listen to the bass player, might get an idea what you should do from there hehe.
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