I have always read the passage describing Emma's charitable intentions as being JA telling us things directly.

I think I read the word "expect" differently to how you do. When I use the word "expect" it's different to the word "hope". One may hope for extraordinary virtues amongst the poor, but I would not expect it. I may hope for fine weather on the weekend, but expect rain. I agree with you that many extraordinary people have been born into poverty and with little formal education have risen to admiration, fame and fortune in history. I presume you would agree that many ordinary people have been born into poverty and with little formal education have stayed poor, anonymous and obscure. Given a random poor person from Regency England, and not knowing anything more about them, I would *expect* them to be of the latter sort, though I would *hope* they would be of the former. Extraordinary virtue is very unusual amongst the rich or the middle-class, why would the poor be particularly virtuous? There are some people who have romantic views about the virtues of poverty, and how people living in small rural cottages on tight incomes are in touch with nature and not corrupted by the evil allurements of London/New York/Paris/Berlin/etc, what I think JA is saying here is that Emma does not suffer from such romantic visions.

In the more specific case, I think what JA is saying here is that Emma does not expect the cottagers to always save their money and never spend a penny on such luxuries as a pint of beer or a rattle for baby to play with, she does not expect them to always be clean and pietous and resigned to their fates.

As for why Emma is more sympathetic to the cottagers than to Miss Bates, I think this is because Emma does not need to spend her evenings on a regular basis with the cottagers. In chapter 3, we have, when JA is talking about Mrs Bates, Miss Bates and Mrs Goddard spending the evening playing cards with Mr Woodhouse
... the quiet prosings of three such women made her feel that every evening so spent, was indeed one of the long evenings she had fearfully anticipated.
And when Emma talks about Miss Bates to Harriet, Emma gives me the impression that Miss Bates bores her:
Heaven forbid! at least, that I should ever bore people half so much about all the Knightleys together, as she does about Jane Fairfax. One is sick of the very name of Jane Fairfax. Every letter from her is read forty times over; her compliments to all friends go round and round again; and if she does but send her aunt the pattern of a stomacher, or knit a pair of garters for her grandmother, one hears of nothing else for a month. (chpt 10)

Emma does also speak very complimentary of Miss Bates in chapter 10:
Those who can barely live, and who live perforce in a very small, and generally very inferior, society, may well be illiberal and cross. This does not apply, however, to Miss Bates; she is only too good natured and too silly to suit me; but, in general, she is very much to the taste of everybody, though single and though poor. Poverty certainly has not contracted her mind: I really believe, if she had only a shilling in the world, she would be very likely to give away sixpence of it; and nobody is afraid of her: that is a great charm."

I think Emma, for all her faults, does understand herself here. Miss Bates is not to Emma's taste because Miss Bates is silly in her conversation. If the cottagers came and called on Mr Woodhouse several evenings a week, I expect that their individual personalities would play a larger part in Emma's feelings towards them and very possibly she would think them boring too.

I think when Emma criticises Miss Bates for being too good-natured, she means that Miss Bates never comes up with any insight into other people. Generally, undifferentiated niceness is boring. Most movies, plays, novels, involve nasty things happening to people because readers, and presumably the creators, find that more interesting. Miss Bates would be more interesting to Emma if she occasionally criticised, if she showed more variation in her gossip - like Mr Knightley who does see faults in Emma and in Mr Elton.