Here's how I have my FBreader set up regarding fonts and spacing, which pretty much is what Kindle app looks like for the most part.
Text Appearance
Font: Bookerly
Line height: 110
Show two pages in landscape: on
Margins: left 30, right 31, top 20, bottom 26, space between columns 20.
Alignment: Justify
Hyphenate words: on (and this is where FBreader goes overboard and hyphenates probably too much when in Justify mode).
Progress Indicator
Height 20
Horizontal margin 11
Reading progress: as page number and percentage
Show clock: no, the iPad does that natively
Show batter level: also no
Colors: This is up to you
Show chapter marks: yes
Max number of marks: 80
Screen -> Taps zones (this is where FBreader excels, in that you can specify different actions for each customizable tap zone)
ePub-specific Options (this is where I disagree with the previous poster who said FBreader doesn't handle CSS well)
Font size: off (this prevents the book settings from overriding your personal settings, up to you if you want the book to follow CSS exactly).
Text alignment: yes (follow what the book CSS says)
Margins: yes (follow what the book CSS says)
Colors: this is up to your personal preference whether you want to follow what the book CSS says.
The one thing it does not appear to do which you said was a deal-breaker for you is showing the book title at the top of the page while in reading mode. However, if you can live with that and try to remember what book you're reading
you might find the rest of the flexibility worth giving it a shot.